MolNFT v1 · #134260 · protein
C-src V281C bound to N-[3-({6-[(1E)-2-cyano-3-(methylamino)-3-oxoprop- 1-en-1-yl]-7-(2-methoxyethyl)-7H-PYRROLO[2,3-D]PYRIMIDIN-5- YL}ETHYNYL)-4-methylphenyl]-3-(TRIFLUOROMETHYL)BENZAMIDE inhibitor
5SYS · Proto-oncogene tyrosine-protein kinase src: “C-src V281C bound to N-[3-({6-[(1E)-2-cyano-3-(methylamino)-3-oxoprop…”. X-ray diffraction, 1 ligand (72F), 4 pockets (best druggability 0.79). MolNFT v1 #134260 on GenesisL1: 3D…
- PDB
- 5SYS
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- 72F
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 258 | 43% helix, 15% strand | P00523 |
Ligands and binding sites
- 72F · N-[3-({6-[(2S)-2-cyano-3-(methylamino)-3-oxopropyl]-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl}ethynyl)-4-methylphenyl]-3-(trifluoromethyl) benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.79 | 0.81 | 98 | 72F |
| 2 | 423 | 0.72 | 0.82 | 38 | 72F |
| 3 | 67 | 0.33 | 0.76 | 20 | empty |
| 4 | 51 | 0.32 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 405 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5SYS · c-Src V281C bound to N-[3-({6-[(1E)-2-cyano-3-(methylamino)-3-oxoprop-1-en-1-yl]-7-(2-meth… · the same entry in another collection · chain A against A, TM-score 1.00
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 P00523
- Elsewhere: RCSB PDB 5SYS · PDBe 5SYS · UniProt P00523
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