3lc5

Selective Benzothiophine Inhibitors of Factor IXa

Method: X-RAY DIFFRACTION D_max: 66.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Coagulation factor IX

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 227–461 Chain B； UniProt 133–188	Fragment：residues 227-461 Fragment：residues 133-188	CA CALCIUM ION × 1 IZX 1-{4-[(R)-phenyl(3-phenyl-1,2,4-oxadiazol-5-yl)methoxy]-1-benzothiophen-2-yl}methanediamine × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.62 Å R-free 0.277

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3LC5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CFH STRUCTURE OF THE METAL-FREE GAMMA-CARBOXYGLUTAMIC ACID-RICH MEMBRANE BINDING REGION OF FACTOR IX BY TWO-DIMENSIONAL NMR SPECTROSCOPY Deposited 1995-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 47–93（47 aa）	Not recorded	FMT FORMIC ACID × 12	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CFI NMR STRUCTURE OF CALCIUM ION-BOUND GAMMA-CARBOXY-GLUTAMIC ACID-RICH DOMAIN OF FACTOR IX Deposited 1995-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 47–93（47 aa） Fragment：THE GLA AND AROMATIC AMINO ACID STACK DOMAINS, RESIDUES 1 - 47	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.35	Resolution not provided
1EDM EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX Deposited 1996-03-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 92–130（39 aa） Fragment：EPIDERMAL GROWTH FACTOR-LIKE DOMAIN Chain C 92–130（39 aa） Fragment：EPIDERMAL GROWTH FACTOR-LIKE DOMAIN	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.3；pH 7.3	Resolution 1.50 Å
1IXA THE THREE-DIMENSIONAL STRUCTURE OF THE FIRST EGF-LIKE MODULE OF HUMAN FACTOR IX: COMPARISON WITH EGF AND TGF-A Deposited 1991-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–130（39 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1MGX COAGULATION FACTOR, MG(II), NMR, 7 STRUCTURES (BACKBONE ATOMS ONLY) Deposited 1995-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 47–93（47 aa） Fragment：THE GLA AND AROMATIC AMINO ACID STACK DOMAINS FROM RESIDUES 1 - 47	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1NL0 Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody, 10C12 Deposited 2003-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 47–91（45 aa） Fragment：Gla domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 CA CALCIUM ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
1NL0 Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody, 10C12 Deposited 2003-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 47–91（45 aa） Fragment：Gla domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 CA CALCIUM ION × 12	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
1RFN HUMAN COAGULATION FACTOR IXA IN COMPLEX WITH P-AMINO BENZAMIDINE Deposited 1999-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–461（235 aa） Fragment：FRAGMENT EGF2-CATALYTIC DOMAIN Chain B 128–183（56 aa） Fragment：FRAGMENT EGF2-CATALYTIC DOMAIN	Not recorded	CA CALCIUM ION × 1 PBZ P-AMINO BENZAMIDINE × 1 TBU TERTIARY-BUTYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 2.80 Å R-free 0.273
2WPH factor IXa superactive triple mutant Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191 Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461	Mutation：YES	CA CALCIUM ION × 1 1PE PENTAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；22 % PEG 3000, 100 MM BIS/TRIS, PH 6.85	Resolution 1.50 Å R-free 0.267
2WPI factor IXa superactive double mutant Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191 Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461	Mutation：YES	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；24 % PEG 6000 100 MM MES PH 7.1	Resolution 1.99 Å R-free 0.252
2WPJ factor IXa superactive triple mutant, NaCl-soaked Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191 Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461	Mutation：YES	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；22 % PEG 3000 100 MM BIS/TRIS PH 6.85	Resolution 1.60 Å R-free 0.256
2WPK factor IXa superactive triple mutant, ethylene glycol-soaked Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191 Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461	Mutation：YES	CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；22 % PEG 3000 100 MM BIS/TRIS PH 6.85	Resolution 2.21 Å R-free 0.259
2WPL factor IXa superactive triple mutant, EDTA-soaked Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191 Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；22 % PEG 3000 100 MM BIS/TRIS PH 6.85	Resolution 1.82 Å R-free 0.289
2WPM factor IXa superactive mutant, EGR-CMK inhibited Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 133–191（59 aa） Fragment：EGF2 DOMAIN, RESIDUES 133-191 Chain S 227–461（235 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 227-461	Mutation：YES	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.85；22 % PEG 3000 100 MM BIS/TRIS PH 6.85	Resolution 2.00 Å R-free 0.318
3KCG Crystal structure of the antithrombin-factor IXa-pentasaccharide complex Deposited 2009-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 227–461（235 aa） Chain L 131–188（58 aa） Fragment：EGF2	Mutation：S195A	CA CALCIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；0.25M Ammonium sulfate, 19.5% PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.70 Å R-free 0.230
3LC3 Benzothiophene Inhibitors of Factor IXa Deposited 2010-01-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–461（235 aa） Fragment：residues 227-461 Chain B 133–188（56 aa） Fragment：residues 133-188	Not recorded	IYX 1-[5-(3,4-dimethoxyphenyl)-1-benzothiophen-2-yl]methanediamine × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.260
3LC3 Benzothiophene Inhibitors of Factor IXa Deposited 2010-01-09	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 227–461（235 aa） Fragment：residues 227-461 Chain D 133–188（56 aa） Fragment：residues 133-188	Not recorded	IYX 1-[5-(3,4-dimethoxyphenyl)-1-benzothiophen-2-yl]methanediamine × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.260
4WM0 Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with acceptor ligand Deposited 2014-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 92–130（39 aa） Fragment：unp residues 92-130	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350	Resolution 2.37 Å R-free 0.233
4WMA Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Glucose Deposited 2014-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 92–130（39 aa） Fragment：unp residues 92-130	Not recorded	MN MANGANESE (II) ION × 1 UPG URIDINE-5'-DIPHOSPHATE-GLUCOSE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350	Resolution 1.62 Å R-free 0.243
4WMB crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, acceptor ligand and UDP Deposited 2014-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 92–130（39 aa） Fragment：unp residues 92-130	Not recorded	MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350	Resolution 2.05 Å R-free 0.235
4WMI Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex I) Deposited 2014-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 92–130（39 aa） Fragment：unp residues 92-130	Not recorded	MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350	Resolution 1.87 Å R-free 0.226
4WMK Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex II) Deposited 2014-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 92–130（39 aa） Fragment：unp residues 92-130	Not recorded	MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350	Resolution 2.08 Å R-free 0.246
4WN2 Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex III) Deposited 2014-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 92–130（39 aa） Fragment：unp residues 92-130	Not recorded	MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350	Resolution 1.95 Å R-free 0.239
4WNH Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Xylose Deposited 2014-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 92–130（39 aa） Fragment：unp residues 92-130	Not recorded	MN MANGANESE (II) ION × 1 UDX URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350	Resolution 1.95 Å R-free 0.224
4YZU Rapid development of two Factor IXa inhibitors from Hit to Lead Deposited 2015-03-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–461（235 aa） Fragment：Peptidase S1 domain (UNP residue 227-461) Chain B 131–191（61 aa） Fragment：EGF-like 2 domain (UNP residues 131-191)	Mutation：R150A	4K6 N-[2-(5,6-dimethyl-1H-benzimidazol-2-yl)ethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；295 K；0.05 M Tris, pH 7.2, 1.2 M ammonium sulfate, 2.0 M sodium chloride	Resolution 1.41 Å R-free 0.161
4Z0K Rapid development of two Factor IXa inhibitors from Hit to Lead Deposited 2015-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–461（235 aa） Fragment：Peptidase S1 domain (UNP residue 227-461) Chain B 131–191（61 aa） Fragment：EGF-like 2 domain (UNP residues 131-191)	Not recorded	4LN N-[(2R)-10-hydroxy-2,7-dimethyl-1,2,3,4-tetrahydropyrido[1,2-b]indazol-2-yl]-4-(4H-1,2,4-triazol-4-yl)benzamide × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；50 mM Tris, pH 7.2, 1.2 M ammonium sulfate, 2.0 M sodium chloride	Resolution 1.41 Å R-free 0.165
4ZAE Development of a novel class of potent and selective FIXa inhibitors Deposited 2015-04-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–461（235 aa） Fragment：Peptidase S1 domain (UNP residues 227-461) Chain B 131–191（61 aa） Fragment：EG-like 2 domain (UNP residues 131-191)	Mutation：R150A	4M1 2,6-dichloro-N-[(2R)-2-(5,6-dimethyl-1H-benzimidazol-2-yl)-2-phenylethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；50 mM CHES, pH 9.0, 1.3 M tri-sodium citrate and 3 mM compound (cross seeded with crystals grown from 50 mM Tris, pH 7.2, 1.45 M ammonium sulfate, 2.0 M sodium chloride and 3 mM compound)	Resolution 1.86 Å R-free 0.174
5EGM Development of a novel tricyclic class of potent and selective FIXa inhibitors Deposited 2015-10-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–461（235 aa） Chain B 131–191（61 aa） Fragment：UNP residues 131-191	Mutation：A150R	NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 5NY 2-chloranyl-~{N}-[(7~{S})-2-methyl-7-phenyl-10-(1~{H}-1,2,3,4-tetrazol-5-yl)-8,9-dihydro-6~{H}-pyrido[1,2-a]indol-7-yl]-4-(1,2,4-triazol-4-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；50 MM CHES, PH 9.0, 1.3 M TRI-SODIUM REMARK 280 CITRATE AND 3 MM COMPOUND (CROSS SEEDED WITH CRYSTALS GROWN FROM REMARK 280 50 MM TRIS, PH 7.2, 1.45 M AMMONIUM SULFATE, 2.0 M SODIUM REMARK 280 CHLORIDE AND 3 MM COMPOUND)	Resolution 1.84 Å R-free 0.171
5F84 Crystal structure of Drosophila Poglut1 (Rumi) complexed with its glycoprotein product (glucosylated EGF repeat) and UDP Deposited 2015-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 92–130（39 aa） Fragment：UNP residues 92-130	Not recorded	UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 5 BGC beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.62M ammonium sulfate	Resolution 2.50 Å R-free 0.239
5F85 Crystal structure of Drosophila Poglut1 (Rumi) complexed with its substrate protein (EGF repeat) and UDP Deposited 2015-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 92–130（39 aa） Fragment：UNP residues 92-130	Not recorded	UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.62M ammonium sulfate	Resolution 2.15 Å R-free 0.243
5F86 Crystal structure of Drosophila Poglut1 (Rumi) complexed with its substrate protein (EGF repeat) Deposited 2015-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 92–130（39 aa） Fragment：UNP residues 92-130	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.62M ammonium sulfate	Resolution 1.90 Å R-free 0.221
5JB8 Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone Deposited 2016-04-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 134–191（58 aa） Chain S 227–461（235 aa）	Mutation：K98T	CA CALCIUM ION × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 18-20% PEG6000	Resolution 1.45 Å R-free 0.185
5JB9 Crystal structure of factor IXa K98T variant in complex with PPACK Deposited 2016-04-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 134–191（58 aa） Chain S 227–461（235 aa）	Mutation：K98T	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 CA CALCIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；6 mg/mL protein/inhibitor complex 0.1 M MES pH 6.5 18% PEG6000	Resolution 1.30 Å R-free 0.176
5JBA Crystal structure of factor IXa variant V16I K98T Y177T I212V in complex with PPACK Deposited 2016-04-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 134–191（58 aa） Chain S 227–461（235 aa）	Mutation：V16I K98T Y177T I212V	CA CALCIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 18% PEG6000	Resolution 1.40 Å R-free 0.179
5JBB Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with EGR-chloromethylketone Deposited 2016-04-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 134–191（58 aa） Chain S 227–461（235 aa）	Mutation：V16I K98T Y177T I213V	CA CALCIUM ION × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 20% PEG6000	Resolution 1.56 Å R-free 0.190
5JBC Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with PPACK Deposited 2016-04-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 134–191（58 aa） Chain S 227–461（235 aa）	Mutation：V16I K98T Y177T I213V	CA CALCIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 20% PEG6000	Resolution 1.90 Å R-free 0.213
5TNO Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors Deposited 2016-10-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–461（235 aa） Fragment：UNP residues 227-461 Chain B 131–191（61 aa） Fragment：UNP residues 131-191	Not recorded	UNL UNKNOWN LIGAND × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；50 MM CHES, PH 9.0, 1.3 M TRI-SODIUM CITRATE AND 3 MM COMPOUND (CROSS SEEDED WITH CRYSTALS GROWN FROM REMARK 280 50 MM TRIS, PH 7.2, 1.45 M AMMONIUM SULFATE, 2.0 M SODIUM REMARK 280 CHLORIDE AND 3 MM COMPOUND)	Resolution 1.54 Å R-free 0.158
5TNT Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors Deposited 2016-10-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–461（235 aa） Fragment：UNP residues 227-461 Chain B 131–191（61 aa） Fragment：UNP residues 131-191	Mutation：R150A	7GQ N-[(1S,4S,7R)-2-(3-amino-4-chloro[1,2]oxazolo[5,4-c]pyridin-7-yl)-2-azabicyclo[2.2.1]heptan-7-yl]-2-chloro-4-(3-methyl-1H-1,2,4-triazol-1-yl)benzamide × 1 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；50 MM CHES, PH 9.0, 1.3 M TRI-SODIUM CITRATE AND 3 MM COMPOUND (CROSS SEEDED WITH CRYSTALS GROWN FROM REMARK 280 50 MM TRIS, PH 7.2, 1.45 M AMMONIUM SULFATE, 2.0 M SODIUM CHLORIDE AND 3 MM COMPOUND)	Resolution 1.40 Å R-free 0.161
5VYG Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide Deposited 2017-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 92–130（39 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 8.5, 15% Glycerol, 1.6 M (NH4)2SO4, 5% 2,2,2-Trifluoroethanol	Resolution 2.20 Å R-free 0.259
5VYG Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide Deposited 2017-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–130（39 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 8.5, 15% Glycerol, 1.6 M (NH4)2SO4, 5% 2,2,2-Trifluoroethanol	Resolution 2.20 Å R-free 0.259
5VYG Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide Deposited 2017-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain C 92–130（39 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 8.5, 15% Glycerol, 1.6 M (NH4)2SO4, 5% 2,2,2-Trifluoroethanol	Resolution 2.20 Å R-free 0.259
6MV4 CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR IXa Deposited 2018-10-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain H 227–461（235 aa） Chain L 133–185（53 aa）	Not recorded	SO4 SULFATE ION × 24 EDO 1,2-ETHANEDIOL × 8 FMT FORMIC ACID × 4 PBZ P-AMINO BENZAMIDINE × 4 CA CALCIUM ION × 4 NA SODIUM ION × 4 CL CHLORIDE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG4000, 1 M NaCl, 0.2 M Ammonium Sulfate, 5 mM Calcium Chloride	Resolution 1.37 Å R-free 0.210
6RFK Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant) Deposited 2019-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 130–191（62 aa） Chain S 227–461（235 aa）	Not recorded	B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；297 K；0.1M BIS-TRIS propane pH 8.5, 24% PEG 3350, 0.275M Na Malonate	Resolution 1.60 Å R-free 0.163
6X5J Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors Deposited 2020-05-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–461（235 aa） Chain B 131–191（61 aa）	Not recorded	GOL GLYCEROL × 2 6NH 2-(4-HYDROXY-5-PHENYL-1H-PYRAZOL-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 NA SODIUM ION × 1 CIT CITRIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1M CITRIC ACID, 20% PEG 6000	Resolution 2.51 Å R-free 0.225
6X5L Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors Deposited 2020-05-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–460（234 aa） Chain B 131–191（61 aa）	Not recorded	UQG 4-{[5-hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide × 1 NA SODIUM ION × 1 CIT CITRIC ACID × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1M CITRIC ACID, 20% PEG 6000	Resolution 2.25 Å R-free 0.233
6X5P Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors Deposited 2020-05-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 227–461（235 aa） Chain B 131–191（61 aa）	Mutation：A138R	UQD 3-chloro-4-{[5-hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide × 1 CIT CITRIC ACID × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1 M CITRIC ACID, 20% PEG 6000	Resolution 2.00 Å R-free 0.239
7AHV Anti-FIXa Fab of mim8 in complex with human FIXa Deposited 2020-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 227–461（235 aa） Chain L 131–188（58 aa）	Not recorded	SO4 SULFATE ION × 17 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；2 M ammonium sulphate, 0.1 M Hepes, pH 7.5	Resolution 3.11 Å R-free 0.283
8EPC Crystal structure of human coagulation factor IXa (S195A), apo-form Deposited 2022-10-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 130–190（61 aa） Fragment：furin cleavage site (RRKR) inserted Chain B 227–461（235 aa）	Mutation：S195A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% Glycerol Ethoxylate	Resolution 2.51 Å R-free 0.281
8EPH Crystal structure of human coagulation factor IXa (S195A), apo-form, DES-GLA Deposited 2022-10-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 93–190（98 aa） Fragment：furin cleavage site (RRKR) inserted Chain B 227–461（235 aa）	Mutation：S195A	FUC alpha-L-fucopyranose × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Na Citrate pH 5.0; 30% Jeffamine ED-2001 pH 7.0	Resolution 1.88 Å R-free 0.211
8EPH Crystal structure of human coagulation factor IXa (S195A), apo-form, DES-GLA Deposited 2022-10-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 93–190（98 aa） Fragment：furin cleavage site (RRKR) inserted Chain D 227–461（235 aa）	Mutation：S195A	FUC alpha-L-fucopyranose × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Na Citrate pH 5.0; 30% Jeffamine ED-2001 pH 7.0	Resolution 1.88 Å R-free 0.211
8EPK Complex of anticoagulant RNA aptamer and human coagulation factor IXa (S195A) Deposited 2022-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 130–190（61 aa） Fragment：furin cleavage site (RRKR) inserted Chain B 227–461（235 aa）	Mutation：S195A	CA CALCIUM ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；60 mM Na Citrate pH 5.0; 4% Tacsimate pH 7.0; 23% PEG 8000	Resolution 2.65 Å R-free 0.261
8EPK Complex of anticoagulant RNA aptamer and human coagulation factor IXa (S195A) Deposited 2022-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain C 130–190（61 aa） Fragment：furin cleavage site (RRKR) inserted Chain D 227–461（235 aa）	Mutation：S195A	CA CALCIUM ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；60 mM Na Citrate pH 5.0; 4% Tacsimate pH 7.0; 23% PEG 8000	Resolution 2.65 Å R-free 0.261
8OL9 Anti-FIXa Fab in complex with human des-(Gla-EGF1) FIXa Deposited 2023-03-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 227–461（235 aa） Chain L 131–188（58 aa）	Not recorded	SO4 SULFATE ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CA CALCIUM ION × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；0.5 M ammonium sulphate, 0.1 M sodium citrate, pH 5.6, !.0 M lithium sulphate	Resolution 2.60 Å R-free 0.323
9BVK Vitamin K-dependent gamma-carboxylase with factor IX propeptide and glutamate-rich region and with vitamin K hydroquinone Deposited 2024-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 29–92（64 aa） Fragment：residues 29-92	Not recorded	A1AVC vitamin K1 hydroquinone × 1 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9BVR Vitamin K-dependent gamma-carboxylase with factor IX propeptide and partially carboxylated glutamate-rich region and with vitamin K hydroquinone and calcium Deposited 2024-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 29–92（64 aa） Fragment：residues 29-92	Not recorded	A1AVC vitamin K1 hydroquinone × 1 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9L21 cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX Deposited 2024-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 29–56（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1AVC vitamin K1 hydroquinone × 1 BCT BICARBONATE ION × 1 CO2 CARBON DIOXIDE × 1 CLR CHOLESTEROL × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.62 Å
9L25 cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX(Gla) Deposited 2024-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 29–56（28 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1AVC vitamin K1 hydroquinone × 1 CLR CHOLESTEROL × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 1 CO2 CARBON DIOXIDE × 1 BCT BICARBONATE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.41 Å
9L6Q Vitamin K-dependent gamma-carboxylase in complex with Coagulation factor IX and vitamin K Deposited 2024-12-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–461（461 aa）	Not recorded	6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 CLR CHOLESTEROL × 1 1L3 Menaquinone-4 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9L6R double-mutant (K217A & K218A) Vitamin K-dependent gamma-carboxylase in complex with Coagulation factor IX and vitamin K Deposited 2024-12-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–461（461 aa）	Not recorded	A1EMC 2-methyl-3-[(2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]naphthalene-1,4-diol × 1 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.59 Å
9WF3 Cryo-EM structure of GGCX-FIX complex Deposited 2025-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 29–56（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 MX7 (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate × 1 CLR CHOLESTEROL × 1 A1AT1 (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.65 Å
9WFN Cryo-EM structure of GGCX-proP2 Deposited 2025-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 29–44（16 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 MX7 (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate × 1 CLR CHOLESTEROL × 1 A1AT1 (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å

55 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FA9_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–235； UniProt 227–461 Author chain B； PDBConstruct 2–57； UniProt 133–188

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3lc5
Deposition date deposition_date	2010-01-09
Structure title title	Selective Benzothiophine Inhibitors of Factor IXa
Keywords keywords	;Protein-Inhibitor complex, Peptidase S1, Blood coagulation, Calcium, Cleavage on pair of basic residues, Disease mutation, Disulfide bond, EGF-like domain, Gamma-carboxyglutamic acid, Glycoprotein, Hemophilia, Hydrolase, Hydroxylation, Pharmaceutical, Phosphoprotein, Polymorphism, Protease, Secreted, Serine protease, Sulfation, Zymogen, Hydrolase-Hydrolase Inhibitor complex ;; Hydrolase/Hydrolase Inhibitor
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.09 Å
Radius of gyration Rg (electron density) rg_electron	18.90 Å
Forward intensity I(0) i0	19084100.00
Molecular weight molecular_weight	32542.0 kDa
Excluded volume excluded_volume	40515 Å³
Envelope volume envelope_volume	47309 Å³
Hydration-shell volume shell_volume	20669 Å³
Envelope diameter envelope_diameter	67.8 Å
Shell Rg shell_rg	25.78 Å
Envelope Rg envelope_rg	19.43 Å
Shape Rg shape_rg	18.83 Å
Total Rg total_rg	20.06 Å
Total atoms total_atoms	2283
Residues n_residues	281
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	66.6 Å
Rg (real space) rg_real	20.01 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	1.9080e+07
I(0) uncertainty (real space) i0_real_error	2.4860e+05
Rg (reciprocal space) rg_reciprocal	20.02 Å
I(0) (reciprocal space) i0_reciprocal	19080000.0000
Solution quality estimate total_estimate	0.8088
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.240
Kurtosis Kurtosis kurtosis	-0.329
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5367000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Coagulation factor IX
Molecular weight formula_weight	26190.8 kDa
EC 编号 ec_number	3.4.21.22
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2296

VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Coagulation factor IX
Molecular weight formula_weight	6256.1 kDa
EC 编号 ec_number	3.4.21.22
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1-{4-[(R)-phenyl(3-phenyl-1,2,4-oxadiazol-5-yl)methoxy]-1-benzothiophen-2-yl}methanediamine
Molecular weight formula_weight	428.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3lc5a_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d3lc5b_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.1 — EGF-type module

CATH v4.4 (3 domains)

Domain ID domain_id	3lc5A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3lc5A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3lc5B00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

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8. Citations (1)

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Unit-cell length a length_a	43.120 Å
Unit-cell length b length_b	65.738 Å
Unit-cell length c length_c	93.985 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.620 Å
Low-resolution limit resolution_low	94.070 Å
R factor r_factor	0.2130
R_work r_work	0.2060
R_free r_free	0.2770

fit	/app/data/saxs_computation/lc/3lc5/3lc5.fit
pddf	/app/data/pr_computation/lc/3lc5/3lc5.pr.out
profile	/app/data/saxs_computation/lc/3lc5/3lc5.dat

Selective Benzothiophine Inhibitors of Factor IXa

1. Protein Identity and Related Structures Protein Identity & Related Structures

Coagulation factor IX

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)