3cjg

Crystal structure of VEGFR2 in complex with a 3,4,5-trimethoxy aniline containing pyrimidine

Method: X-RAY DIFFRACTION Dmax: 67.1 Å Quality: EXCELLENT

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

Vascular endothelial growth factor receptor 2

Homo sapiens

UniProt P35968

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 806–939 Chain A; UniProt 994–1168 Fragment:Kinase domain; residues 806-939 and 994-1168 Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 KIM N~4~-methyl-N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;VAPOR DIFFUSION, HANGING DROP Resolution 2.25 Å R-free 0.253

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.

53 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGFR2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–134; UniProt 806–939 Author chain A; PDBConstruct 135–309; UniProt 994–1168

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 3cjg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3cjg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3cjg
Deposition date deposition_date2008-03-12
Structure title titleCrystal structure of VEGFR2 in complex with a 3,4,5-trimethoxy aniline containing pyrimidine
Keywords keywords;Vascular endothelial growth factor receptor 2. vegfr-2, kinase insert domain receptor, protein-tyrosine kinase receptor flk-1, Angiogenesis, ATP-binding, Developmental protein, Differentiation, Glycoprotein, Host-virus interaction, Immunoglobulin domain, Membrane, Nucleotide-binding, Phosphoprotein, Transferase, Transmembrane, Tyrosine-protein kinase ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.12
Radius of gyration Rg (electron density) rg_electron19.98
Forward intensity I(0) i018593300.00
Molecular weight molecular_weight32617.0 kDa
Excluded volume excluded_volume40863 ų
Envelope volume envelope_volume48795 ų
Hydration-shell volume shell_volume20475 ų
Envelope diameter envelope_diameter67.6
Shell Rg shell_rg26.40
Envelope Rg envelope_rg20.33
Shape Rg shape_rg19.98
Total Rg total_rg20.90
Total atoms total_atoms2290
Residues n_residues280
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax67.1
Rg (real space) rg_real21.05
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real1.8590e+07
I(0) uncertainty (real space) i0_real_error2.6150e+05
Rg (reciprocal space) rg_reciprocal21.07
I(0) (reciprocal space) i0_reciprocal18590000.0000
Solution quality estimate total_estimate0.9016
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary66.1
Skewness Skewness skewness0.249
Kurtosis Kurtosis kurtosis-0.477
Angular range angular_range— – 0.3750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5549000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.991

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3cjga_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id3cjgA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3cjgA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)