MolNFT v1 · #122350 · protein
Crystal structure of P21-activated kinase 1 (PAK1) in complex with compound 9
5IME · SERINE/THREONINE-protein kinase pak 1: “Crystal structure of P21-activated kinase 1 (PAK1) in complex with compound 9”. X-ray diffraction, 1 ligand (6BZ), 5 pockets (best druggability 0.76). MolNFT v1 #122350 on GenesisL1: 3D…
- PDB
- 5IME
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pak 1
- EC
- 2.7.11.1
- UniProt
- Q13153
- Ligands
- 6BZ
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 280 | 44% helix, 14% strand | Q13153 |
| B | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 280 | 41% helix, 16% strand | Q13153 |
Ligands and binding sites
- 6BZ · 8-(3-aminopropyl)-6-[2-chloro-4-(3-methyl-2-oxopyrazin-1(2H)-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.76 | 0.79 | 82 | 6BZ |
| 2 | 485 | 0.67 | 0.78 | 41 | 6BZ |
| 3 | 237 | 0.52 | 0.76 | 34 | empty |
| 4 | 51 | 0.30 | 0.76 | 13 | empty |
| 5 | 61 | 0.29 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 928 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5IME · Crystal structure of P21-activated kinase 1 (PAK1) in complex with compound 9 · the same entry in another collection · chain A against A, TM-score 1.00
- Q13153 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pak 1 (Q13153) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q13153
- Elsewhere: RCSB PDB 5IME · PDBe 5IME · UniProt Q13153
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