MolNFT v1 · #116023 · protein
Kinase domain of csrc in complex with RL40
5D12 · Proto-oncogene tyrosine-protein kinase src: “Kinase domain of csrc in complex with RL40”. X-ray diffraction, 1 ligand (G97), 5 pockets (best druggability 0.69). MolNFT v1 #116023 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5D12
- Type
- protein
- Length
- 513 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
- G97
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 260 | 37% helix, 14% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 253 | 35% helix, 15% strand | P00523 |
Ligands and binding sites
- G97 · N-[2-phenyl-4-(1H-pyrazol-3-ylamino)quinazolin-7-yl]prop-2-enamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.69 | 0.77 | 67 | G97 |
| 2 | 375 | 0.63 | 0.78 | 39 | G97 |
| 3 | 385 | 0.60 | 0.76 | 44 | empty |
| 4 | 98 | 0.58 | 0.85 | 19 | empty |
| 5 | 132 | 0.38 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 403 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5D12 · Kinase domain of cSrc in complex with RL40 · 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 5D12 · PDBe 5D12 · UniProt P00523
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