SAXSdb — 3hng

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

Vascular endothelial growth factor receptor 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 801–1158	Fragment：KINASE DOMAIN, UNP residues 801-1158	8ST N-(4-chlorophenyl)-2-[(pyridin-4-ylmethyl)amino]benzamide × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M potassium formate, 20% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.260

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 3HNG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FLT VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1997-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 132–226（95 aa） Fragment：SECOND EXTRACELLULAR IGG LIKE DOMAIN, RESIDUES 129 - 229 Chain Y 132–226（95 aa） Fragment：SECOND EXTRACELLULAR IGG LIKE DOMAIN, RESIDUES 129 - 229	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.70 Å R-free 0.261
1FLT VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1997-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain X 132–226（95 aa） Fragment：SECOND EXTRACELLULAR IGG LIKE DOMAIN, RESIDUES 129 - 229 Chain Y 132–226（95 aa） Fragment：SECOND EXTRACELLULAR IGG LIKE DOMAIN, RESIDUES 129 - 229	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.70 Å R-free 0.261
1QSV THE VEGF-BINDING DOMAIN OF FLT-1, 20 NMR STRUCTURES Deposited 1999-06-23	Different construct 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 129–229（101 aa） Fragment：SECOND EXTRACELLULAR IMMUNOGLOBULIN-LIKE DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.7；300 K；Ionic strength (raw mmCIF value) 150mM；Pressure AMBIENT NMR sample composition 1MM FLT-1(DOMAIN2) U-15N,13C; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS NMR sample composition 1MM FLT-1(DOMAIN2) U-15N; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS	Resolution not provided
1QSZ THE VEGF-BINDING DOMAIN OF FLT-1 (MINIMIZED MEAN) Deposited 1999-06-24	Different construct 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 129–229（101 aa） Fragment：SECOND EXTRACELLULAR IMMUNOGLOBULIN-LIKE DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.7；300 K；Ionic strength (raw mmCIF value) 150mM；Pressure AMBIENT NMR sample composition 1MM FLT-1(DOMAIN2) U-15N,13C; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS NMR sample composition 1MM FLT-1(DOMAIN2) U-15N; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS NMR sample composition 1MM FLT-1(DOMAIN2) 15% 13C; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS	Resolution not provided
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 129–229（101 aa） Fragment：DOMAIN 2 Chain Y 129–229（101 aa） Fragment：DOMAIN 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.284
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain T 129–229（101 aa） Fragment：DOMAIN 2 Chain U 129–229（101 aa） Fragment：DOMAIN 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.284
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain T 129–229（101 aa） Fragment：DOMAIN 2 Chain U 129–229（101 aa） Fragment：DOMAIN 2 Chain X 129–229（101 aa） Fragment：DOMAIN 2 Chain Y 129–229（101 aa） Fragment：DOMAIN 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.284
1RV6 Crystal Structure of PlGF in Complex with Domain 2 of VEGFR1 Deposited 2003-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 130–229（100 aa） Fragment：domain-2 Chain Y 130–229（100 aa） Fragment：domain-2	Not recorded	B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.45 Å R-free 0.260
2XAC Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity Deposited 2010-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 129–226（98 aa） Fragment：DOMAIN 2, RESIDUES 129-226 Chain X 129–226（98 aa） Fragment：DOMAIN 2, RESIDUES 129-226	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；14% PEG 4000, 0.1M SODIUM CITRATE, PH 5.6 AND 0.2M LICL	Resolution 2.71 Å R-free 0.364
4CKV Crystal structure of VEGFR-1 domain 2 in presence of Zn Deposited 2014-01-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain X 132–225（94 aa） Fragment：DOMAIN-2, RESIDUES 132-225	Not recorded	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；VAPOR DIFFUSION METHOD, MOTHER LIQUOR:1MM VEGFR-1-D2,0.1%(W/V) DDM,4MM LAXAPHYCINE-A,5MM HEPES/NAOH PH 7.5. RESERVOIR:18% (W/V) PEG8000,100MM HEPES/NAOH PH 7.5, 18C	Resolution 2.06 Å R-free 0.205
4CL7 Crystal structure of VEGFR-1 domain 2 in presence of Cobalt Deposited 2014-01-13	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 132–225（94 aa） Fragment：DOMAIN-2, RESIDUES 132-225 Chain C 132–225（94 aa） Fragment：DOMAIN-2, RESIDUES 132-225	Not recorded	CO COBALT (II) ION × 3 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTAL WERE OBTAINED BY HANGING DROP METHOD FROM 1MM VEGFR1-D2, 5MM HEPES/NAOH PH7.0, 10MM COCL2, 100 MM BIS-TRIS/HCL PH6.5 15%(W/V) PEG3350.	Resolution 2.00 Å R-free 0.233
4CL7 Crystal structure of VEGFR-1 domain 2 in presence of Cobalt Deposited 2014-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 132–225（94 aa） Fragment：DOMAIN-2, RESIDUES 132-225 Chain D 132–225（94 aa） Fragment：DOMAIN-2, RESIDUES 132-225	Not recorded	CO COBALT (II) ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTAL WERE OBTAINED BY HANGING DROP METHOD FROM 1MM VEGFR1-D2, 5MM HEPES/NAOH PH7.0, 10MM COCL2, 100 MM BIS-TRIS/HCL PH6.5 15%(W/V) PEG3350.	Resolution 2.00 Å R-free 0.233
5ABD CRYSTAL STRUCTURE OF VEGFR-1 DOMAIN 2 IN PRESENCE OF CU Deposited 2015-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 132–226（95 aa） Fragment：DOMAIN-2, RESIDUES 132-226	Not recorded	NA SODIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；VAPOR DIFFUSION METHOD, MOTHER LIQUOR: 1.5MICROM VERGFR1-D2, 15MM TRIS/HCL PH 8.1, 25MM NACL, 5MM CUSO4 RESERVOIR: 19.5% (W/V) PEG8000, 100MM SA,	Resolution 2.00 Å R-free 0.222
5ABD CRYSTAL STRUCTURE OF VEGFR-1 DOMAIN 2 IN PRESENCE OF CU Deposited 2015-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 132–226（95 aa） Fragment：DOMAIN-2, RESIDUES 132-226	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；VAPOR DIFFUSION METHOD, MOTHER LIQUOR: 1.5MICROM VERGFR1-D2, 15MM TRIS/HCL PH 8.1, 25MM NACL, 5MM CUSO4 RESERVOIR: 19.5% (W/V) PEG8000, 100MM SA,	Resolution 2.00 Å R-free 0.222
5ABD CRYSTAL STRUCTURE OF VEGFR-1 DOMAIN 2 IN PRESENCE OF CU Deposited 2015-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 132–226（95 aa） Fragment：DOMAIN-2, RESIDUES 132-226	Not recorded	NA SODIUM ION × 1 SO4 SULFATE ION × 1 CU COPPER (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；VAPOR DIFFUSION METHOD, MOTHER LIQUOR: 1.5MICROM VERGFR1-D2, 15MM TRIS/HCL PH 8.1, 25MM NACL, 5MM CUSO4 RESERVOIR: 19.5% (W/V) PEG8000, 100MM SA,	Resolution 2.00 Å R-free 0.222
5T89 Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6 Deposited 2016-09-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 27–656（630 aa） Chain Y 27–656（630 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；10-14% PEG3000 200 mM calcium chloride 100 mM MES pH 6.5	Resolution 4.00 Å R-free 0.315

10 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGFR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–360； UniProt 801–1158

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3hng
Deposition date deposition_date	2009-05-31
Structure title title	Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide
Keywords keywords	;RECEPTOR TYROSINE KINASE, VEGFR1, FLT1, KINASE DOMAIN, INHIBITOR, ACTIVATION LOOP, VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, SGC STOCKHOLM, Angiogenesis, ATP-binding, Cell membrane, Developmental protein, Differentiation, Disulfide bond, Glycoprotein, Immunoglobulin domain, Kinase, Membrane, Nucleotide-binding, Phosphoprotein, Receptor, Secreted, Transferase, Transmembrane, Tyrosine-protein kinase ;; TRANSFERASE
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	20.31 Å
Radius of gyration Rg (electron density) rg_electron	19.20 Å
Forward intensity I(0) i0	18452100.00
Molecular weight molecular_weight	33006.0 kDa
Excluded volume excluded_volume	41578 Å³
Envelope volume envelope_volume	48871 Å³
Hydration-shell volume shell_volume	20922 Å³
Envelope diameter envelope_diameter	65.7 Å
Shell Rg shell_rg	25.87 Å
Envelope Rg envelope_rg	19.55 Å
Shape Rg shape_rg	19.19 Å
Total Rg total_rg	20.20 Å
Total atoms total_atoms	2315
Residues n_residues	288
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	65.8 Å
Rg (real space) rg_real	20.23 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	1.8450e+07
I(0) uncertainty (real space) i0_real_error	2.2870e+05
Rg (reciprocal space) rg_reciprocal	20.25 Å
I(0) (reciprocal space) i0_reciprocal	18450000.0000
Solution quality estimate total_estimate	0.8113
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.245
Kurtosis Kurtosis kurtosis	-0.367
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6578000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Vascular endothelial growth factor receptor 1
Molecular weight formula_weight	41081.1 kDa
EC 编号 ec_number	2.7.10.1
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	2357

SMPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTHIGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLL

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 non-polymer

Description description	N-(4-chlorophenyl)-2-[(pyridin-4-ylmethyl)amino]benzamide
Molecular weight formula_weight	337.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3hngA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3hngA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	58.040 Å
Unit-cell length b length_b	71.150 Å
Unit-cell length c length_c	196.020 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	44.990 Å
R factor r_factor	0.1974
R_work r_work	0.1943
R_free r_free	0.2602

fit	/app/data/saxs_computation/hn/3hng/3hng.fit
pddf	/app/data/pr_computation/hn/3hng/3hng.pr.out
profile	/app/data/saxs_computation/hn/3hng/3hng.dat

Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide

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

Vascular endothelial growth factor receptor 1

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