MolNFT v1 · #82595 · protein
Crystal structure of hck complexed with a pyrrolo-pyrimidine inhibitor 4-amino-5-(4-phenoxyphenyl)-7H-PYRROLO[2,3-D]PYRIMIDIN-7-yl- cyclopentane
3VRY · Tyrosine-protein kinase hck: “Crystal structure of hck complexed with a pyrrolo-pyrimidine inhibitor…”. X-ray diffraction, 3 ligands (B43, CA, CL), 11 pockets (best druggability 0.79). MolNFT v1 #82595 on GenesisL1: 3D structure…
- PDB
- 3VRY
- Type
- protein
- Length
- 864 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase hck
- EC
- 2.7.10.2
- UniProt
- P08631
- Ligands
- B43, CA, CL
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase hck (EC 2.7.10.2) | protein | 429 | 30% helix, 24% strand | P08631 |
| B | Tyrosine-protein kinase hck (EC 2.7.10.2) | protein | 435 | 29% helix, 25% strand | P08631 |
Ligands and binding sites
- B43 · 4-Amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl-cyclopentane · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.79 | 0.81 | 123 | empty |
| 2 | 1071 | 0.76 | 0.79 | 84 | empty |
| 3 | 509 | 0.72 | 0.80 | 49 | B43 |
| 4 | 465 | 0.70 | 0.81 | 45 | B43 |
| 5 | 86 | 0.47 | 0.82 | 20 | CA |
Interfaces
1 interface between chains.
- A–B · 1077 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3VRY · Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P08631 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase hck (P08631) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P08631
- Elsewhere: RCSB PDB 3VRY · PDBe 3VRY · UniProt P08631
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