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5jfr

Potent, Reversible MetAP2 Inhibitors via Fragment Based Drug Discovery

Method: X-RAY DIFFRACTION Dmax: 69.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Methionine aminopeptidase 2

Homo sapiens

UniProt P50579

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 87–455 Fragment：UNP residues 87-455 MN MANGANESE (II) ION × 2 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 1 6KP 7-fluoro-4-(5-methyl-3H-imidazo[4,5-b]pyridin-6-yl)-2,4-dihydropyrazolo[4,3-b]indole × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；40% MPD, 0.1M Hepes pH 7.0 Resolution 1.60 Å R-free 0.171

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 5JFR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B59 COMPLEX OF HUMAN METHIONINE AMINOPEPTIDASE-2 COMPLEXED WITH OVALICIN Deposited 1999-01-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 109–478（370 aa）
Not recorded CO COBALT (II) ION × 2 OVA 3,4-DIHYDROXY-2-METHOXY-4-METHYL-3-[2-METHYL-3-(3-METHYL-BUT-2-ENYL) -OXIRANYL]-CYCLOHEXANONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.4；15-30% T-BUTANOL, 50MM CITRATE BUFFER PH=5.2-5.4
Resolution 1.80 Å R-free 0.222
1B6A HUMAN METHIONINE AMINOPEPTIDASE 2 COMPLEXED WITH TNP-470 Deposited 1999-01-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–478（478 aa）
Not recorded CO COBALT (II) ION × 2 TN4 (1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.4；pH 5.40
Resolution 1.60 Å R-free 0.216
1BN5 HUMAN METHIONINE AMINOPEPTIDASE 2 Deposited 1998-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–478（478 aa）
Not recorded CO COBALT (II) ION × 2 TBU TERTIARY-BUTYL ALCOHOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.4；pH 5.4
Resolution 1.80 Å R-free 0.228
1BOA HUMAN METHIONINE AMINOPEPTIDASE 2 COMPLEXED WITH ANGIOGENESIS INHIBITOR FUMAGILLIN Deposited 1998-08-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–478（478 aa）
Not recorded CO COBALT (II) ION × 2 FUG FUMAGILLIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.4；pH 5.4
Resolution 1.80 Å R-free 0.232
1KQ0 Human methionine aminopeptidase type II in complex with D-methionine Deposited 2002-01-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–478（478 aa）
Not recorded ZN ZINC ION × 2 MED D-METHIONINE × 1 TBU TERTIARY-BUTYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；18-23% t-butanol in 70 mM sodium citrate buffer, pH 5.3 to 5.6, 3 mM DTT (DL-dithiothreitol), VAPOR DIFFUSION, SITTING DROP at 277K, pH 5.5
Resolution 2.00 Å R-free 0.218
1KQ9 Human methionine aminopeptidase type II in complex with L-methionine Deposited 2002-01-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–478（478 aa）
Not recorded ZN ZINC ION × 2 MET METHIONINE × 1 TBU TERTIARY-BUTYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；18-23% t-butanol in 70 mM sodium citrate buffer, pH 5.3 to 5.6, 3 mM DTT (DL-dithiothreitol), VAPOR DIFFUSION, SITTING DROP at 277K, pH 5.5
Resolution 1.90 Å R-free 0.207
1QZY Human Methionine Aminopeptidase in complex with bengamide inhibitor LAF153 and cobalt Deposited 2003-09-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–478（478 aa）
Not recorded CO COBALT (II) ION × 2 TDE (E)-(2R,3R,4S,5R)-3,4,5-TRIHYDROXY-2-METHOXY-8,8-DIMETHYL-NON-6-ENOIC ACID ((3S,6R)-6-HYDROXY-2-OXO-AZEPAN-3-YL)-AMIDE × 1 TBU TERTIARY-BUTYL ALCOHOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å R-free 0.211
1R58 Crystal Structure of MetAP2 complexed with A357300 Deposited 2003-10-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa） Fragment：residues 110-478
Not recorded MN MANGANESE (II) ION × 2 AO5 N'-((2S,3R)-3-AMINO-2-HYDROXY-5-(ISOPROPYLSULFANYL)PENTANOYL)-N-3-CHLOROBENZOYL HYDRAZIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；isopropyl alcohol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.247
1R5G Crystal Structure of MetAP2 complexed with A311263 Deposited 2003-10-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa） Fragment：residues 110-478
Not recorded MN MANGANESE (II) ION × 2 AO1 (2S,3R)-3-AMINO-2-HYDROXY-5-(ETHYLSULFANYL)PENTANOYL-((S)-(-)-(1-NAPHTHYL)ETHYL)AMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.00 Å R-free 0.259
1R5H Crystal Structure of MetAP2 complexed with A320282 Deposited 2003-10-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa） Fragment：residues 110-478
Not recorded MN MANGANESE (II) ION × 2 AO2 N'-(2S,3R)-3-AMINO-4-CYCLOHEXYL-2-HYDROXY-BUTANO-N-(4-METHYLPHENYL)HYDRAZIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.248
1YW7 h-MetAP2 complexed with A444148 Deposited 2005-02-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa）
Not recorded MN MANGANESE (II) ION × 2 A41 5-METHYL-2-[(PHENYLSULFONYL)AMINO]BENZOIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.85 Å R-free 0.248
1YW8 h-MetAP2 complexed with A751277 Deposited 2005-02-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa）
Not recorded MN MANGANESE (II) ION × 2 A75 2-[(PHENYLSULFONYL)AMINO]-5,6,7,8-TETRAHYDRONAPHTHALENE-1-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.65 Å R-free 0.273
1YW9 h-MetAP2 complexed with A849519 Deposited 2005-02-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa）
Not recorded MN MANGANESE (II) ION × 2 A84 2-[({2-[(1Z)-3-(DIMETHYLAMINO)PROP-1-ENYL]-4-FLUOROPHENYL}SULFONYL)AMINO]-5,6,7,8-TETRAHYDRONAPHTHALENE-1-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.64 Å R-free 0.246
2ADU Human Methionine Aminopeptidase Complex with 4-Aryl-1,2,3-triazole Inhibitor Deposited 2005-07-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa） Fragment：residues 110-478
Mutation：V347I CO COBALT (II) ION × 2 R20 4-(3-METHYLPHENYL)-1H-1,2,3-TRIAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.4；274 K；100 MM CITRATE BUFFER, 30% BUTANOL, pH 5.4, VAPOR DIFFUSION, temperature 274 K, pH 5.40
Resolution 1.90 Å R-free 0.355
2EA2 h-MetAP2 complexed with A773812 Deposited 2007-01-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa） Fragment：residues 110-478
Not recorded MN MANGANESE (II) ION × 2 F77 3-ETHYL-6-{[(4-FLUOROPHENYL)SULFONYL]AMINO}-2-METHYLBENZOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20-30 % isopropanol, 0.1M Na citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.255
2EA4 h-MetAP2 complexed with A797859 Deposited 2007-01-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa） Fragment：residues 110-478
Not recorded MN MANGANESE (II) ION × 2 F79 2-(2-AMINOETHOXY)-3-ETHYL-6-{[(4-FLUOROPHENYL)SULFONYL]AMINO}BENZOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20-30 % isopropanol, 0.1M Na citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.35 Å R-free 0.272
2GA2 h-MetAP2 complexed with A193400 Deposited 2006-03-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa）
Not recorded MN MANGANESE (II) ION × 2 A19 5-BROMO-2-{[(4-CHLOROPHENYL)SULFONYL]AMINO}BENZOIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å R-free 0.251
2OAZ Human Methionine Aminopeptidase-2 Complexed with SB-587094 Deposited 2006-12-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–478（369 aa）
Not recorded CO COBALT (II) ION × 2 I96 N-(2-ISOPROPYLPHENYL)-3-[(2-THIENYLMETHYL)THIO]-1H-1,2,4-TRIAZOL-5-AMINE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.287
5CLS Structure of human methionine aminopeptidase-2 complexed with spiroepoxytriazole inhibitor (+)-31a Deposited 2015-07-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa） Fragment：UNP residues 108-478
Not recorded CO COBALT (II) ION × 1 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 2 52T (4R,7R)-7-hydroxy-1-(4-methoxybenzyl)-7-methyl-4,5,6,7-tetrahydro-1H-benzotriazol-4-yl propan-2-ylcarbamate × 1 CIT CITRIC ACID × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；292 K；Na Citrate, Tert-butanol
Resolution 1.75 Å R-free 0.189
5D6E Structure of human methionine aminopeptidase 2 with covalent spiroepoxytriazole inhibitor (-)-31b Deposited 2015-08-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa） Fragment：UNP residues 108-478
Not recorded 94A (4R,7S)-7-hydroxy-1-(4-methoxybenzyl)-7-methyl-4,5,6,7-tetrahydro-1H-benzotriazol-4-yl propan-2-ylcarbamate × 1 CO COBALT (II) ION × 2 TBU TERTIARY-BUTYL ALCOHOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；292 K；Na Citrate, Tert-butanol
Resolution 1.49 Å R-free 0.156
5D6F Structure of human methionine aminopeptidase-2 complexed with spiroepoxytriazole inhibitor (+)-31b Deposited 2015-08-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded 57R (4S,7R)-7-hydroxy-1-(4-methoxybenzyl)-7-methyl-4,5,6,7-tetrahydro-1H-benzotriazol-4-yl propan-2-ylcarbamate × 1 CO COBALT (II) ION × 1 TBU TERTIARY-BUTYL ALCOHOL × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；292 K；Na Citrate, Tert-butanol
Resolution 1.55 Å R-free 0.185
5JHU Potent, Reversible MetAP2 Inhibitors via FBDD Deposited 2016-04-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–455（369 aa） Fragment：UNP residues 87-455
Not recorded MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 6KO [(2R)-1-([1,2,4]triazolo[1,5-a]pyrimidin-7-yl)pyrrolidin-2-yl]methyl 2-methoxybenzoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；277 K；30% MPD, 0.05M MES pH 5.9
Resolution 1.80 Å R-free 0.181
5JI6 Potent, Reversible MetAP2 Inhibitors via FBDD Deposited 2016-04-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–455（369 aa） Fragment：UNP residues 87-455
Not recorded MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 1 6KN 4-(3-methylpyridin-4-yl)-6-(trifluoromethyl)-1H-indazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；293 K；24.% PEG MME 2000, 0.05M MES pH 5.9, 0.0175M Ammonium Sulfate
Resolution 2.15 Å R-free 0.230
5LYW CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR 6-((R)-2-o-Tolyloxymethyl-pyrrolidin-1-yl)-9H-purine Deposited 2016-09-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa） Fragment：108-478
Mutation：none 7BH 6-[(2~{R})-2-[(2-methylphenoxy)methyl]pyrrolidin-1-yl]-7~{H}-purine × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；24% methanol, 100 mM citrate
Resolution 1.69 Å R-free 0.193
5LYX CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR 5-((R)-1-[1,2,4]Triazolo[1,5-a]pyrimidin-7-yl-pyrrolidin-2-ylmethoxy)-isoquinoline Deposited 2016-09-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa） Fragment：108-478
Mutation：none 7BF 5-[[(2~{R})-1-([1,2,4]triazolo[1,5-a]pyrimidin-7-yl)pyrrolidin-2-yl]methoxy]isoquinoline × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% methanol, 0.1 M citrate
Resolution 1.90 Å R-free 0.217
6QED CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR (S)-3-Hydroxy-2-oxo-1-(2-oxo-1,2,3,4-tetrahydro-quinolin-6-yl)-pyrrolidine-3-carboxylic acid 3-chloro-5-fluoro-benzylamide Deposited 2019-01-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 HZK (3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-(2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)pyrrolidine-3-carboxamide × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0
Resolution 1.80 Å R-free 0.198
6QEF CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR (S)-3-Hydroxy-2-oxo-1-phenyl-pyrrolidine-3-carboxylic acid 3-chloro-5-fluoro-benzylamide Deposited 2019-01-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 HZW (3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-phenyl-pyrrolidine-3-carboxamide × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0
Resolution 1.79 Å R-free 0.195
6QEG CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR 2-Oxo-1-phenyl-pyrrolidine-3-carboxylic acid (2-thiophen-2-yl-ethyl)-amide Deposited 2019-01-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded GOL GLYCEROL × 1 K4K (3~{S})-3-oxidanyl-2-oxidanylidene-1-phenyl-~{N}-(2-thiophen-2-ylethyl)pyrrolidine-3-carboxamide × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0
Resolution 2.08 Å R-free 0.228
6QEH CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR 5-Chloro-quinolin-8-ol Deposited 2019-01-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded GOL GLYCEROL × 1 HZQ 5-chloranylquinolin-8-ol × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0,
Resolution 2.17 Å R-free 0.220
6QEI CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR 5,6-Difluoro-3-(2-isopropoxy-4-piperazin-1-yl-phenyl)-1H-indole-2-carboxylic acid amide Deposited 2019-01-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 HZE 5,6-bis(fluoranyl)-3-(4-piperazin-1-yl-2-propan-2-yloxy-phenyl)-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0,
Resolution 1.80 Å R-free 0.209
6QEJ CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR Thiophene-2-sulfonic acid (4-fluoro-benzyl)-(4H-[1,2,4]triazol-3-ylmethyl)-amide Deposited 2019-01-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 HZT ~{N}-[(4-fluorophenyl)methyl]-~{N}-(1~{H}-1,2,4-triazol-5-ylmethyl)thiophene-2-sulfonamide × 1 TBU TERTIARY-BUTYL ALCOHOL × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0,
Resolution 1.62 Å R-free 0.184
7A12 CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GW557358X (COMPOUND 9) Deposited 2020-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded PO4 PHOSPHATE ION × 9 QVK 5-chloranyl-3-phenyl-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD)
Resolution 2.00 Å R-free 0.198
7A13 CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK1978537A (COMPOUND 27) Deposited 2020-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded PO4 PHOSPHATE ION × 7 QW5 5-chloranyl-3-(3-methoxyphenyl)-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD).
Resolution 2.04 Å R-free 0.197
7A14 CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2218325A (COMPOUND 32) Deposited 2020-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded PO4 PHOSPHATE ION × 7 QVB 5-chloranyl-6-fluoranyl-3-(2-propan-2-yloxyphenyl)-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD)
Resolution 2.14 Å R-free 0.215
7A15 CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2224863A (COMPOUND 42) Deposited 2020-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded PO4 PHOSPHATE ION × 7 QV5 5-chloranyl-6-fluoranyl-3-(4-piperazin-1-yl-2-propan-2-yloxy-phenyl)-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD)
Resolution 2.15 Å R-free 0.201
7A16 CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2229238A (COMPOUND 43) Deposited 2020-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–478（371 aa）
Not recorded PO4 PHOSPHATE ION × 7 HZE 5,6-bis(fluoranyl)-3-(4-piperazin-1-yl-2-propan-2-yloxy-phenyl)-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD)
Resolution 1.90 Å R-free 0.216
8ONY Human Methionine Aminopeptidase 2 at the 80S ribosome Deposited 2023-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric
Chain A 1–478（478 aa）
Not recorded CO COBALT (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
8OXG Crystal structure of human methionine aminopeptidase-2 complexed with (3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methyl-2-buten-1-yl)-2-oxiranyl]-1-oxaspiro[2.5]oct-6-yl N-(trans-4-aminocyclohexyl)carbamate Deposited 2023-05-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 108–478（371 aa）
Chain B 108–478（371 aa）
Not recorded W5N [(1~{R},2~{S},3~{S},4~{R})-2-methoxy-4-methyl-3-[(2~{R},3~{S})-2-methyl-3-(3-methylbut-2-enyl)oxiran-2-yl]-4-oxidanyl-cyclohexyl] ~{N}-(4-azanylcyclohexyl)carbamate × 2 MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.73 Å R-free 0.215
9FPZ Human NatA-MAP2 80S ribosome complex Deposited 2024-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain A 1–478（478 aa）
Not recorded CO COBALT (II) ION × 2 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å

39 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MAP2_HUMAN
Isoform P50579-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–369； UniProt 87–455

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

SAXS profile for 5jfr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5jfr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5jfr
Deposition date deposition_date2016-04-19
Structure title titlePotent, Reversible MetAP2 Inhibitors via Fragment Based Drug Discovery
Keywords keywordsHydrolase, peptidase, metal ion binding, proteolysis, Hydrolase-Hydrolase Inhibitor complex; Hydrolase/Hydrolase Inhibitor
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.47 Å
Radius of gyration Rg (electron density) rg_electron20.56 Å
Forward intensity I(0) i030600900.00
Molecular weight molecular_weight41594.0 kDa
Excluded volume excluded_volume51630 ų
Envelope volume envelope_volume59585 ų
Hydration-shell volume shell_volume23713 ų
Envelope diameter envelope_diameter71.0 Å
Shell Rg shell_rg27.74 Å
Envelope Rg envelope_rg21.13 Å
Shape Rg shape_rg20.55 Å
Total Rg total_rg21.48 Å
Total atoms total_atoms2909
Residues n_residues366
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.8 Å
Rg (real space) rg_real21.35 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real3.0600e+07
I(0) uncertainty (real space) i0_real_error3.3590e+05
Rg (reciprocal space) rg_reciprocal21.38 Å
I(0) (reciprocal space) i0_reciprocal30600000.0000
Solution quality estimate total_estimate0.7238
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.7 Å
Skewness Skewness skewness0.204
Kurtosis Kurtosis kurtosis-0.430
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10650000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 0.281; Positv: 1.000; Valcen: 1.000; Smooth: 0.975
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5jfrA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily10 — Creatinase/methionine aminopeptidase superfamily
Domain ID domain_id5jfrA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
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8. Citations (1)

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9. Files and Curves (10)