MolNFT v1 · #124319 · protein
PAK1 in complex with bis-anilino pyrimidine inhibitor
5KBQ · SERINE/THREONINE-protein kinase pak 1: “PAK1 in complex with bis-anilino pyrimidine inhibitor”. X-ray diffraction, 1 ligand (IPV), 5 pockets (best druggability 0.67). MolNFT v1 #124319 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KBQ
- Type
- protein
- Length
- 562 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
- IPV
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 289 | 42% helix, 17% strand | Q13153 |
| B | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 273 | 42% helix, 16% strand | Q13153 |
Ligands and binding sites
- IPV · [4-methyl-3-[methyl-[2-[(3-methylsulfonyl-5-morpholin-4-yl-phenyl)amino]pyrimidin-4-yl]amino]phenyl]methanol · ligand · chains A
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 | 451 | 0.67 | 0.79 | 48 | IPV |
| 2 | 400 | 0.66 | 0.79 | 44 | empty |
| 3 | 227 | 0.59 | 0.80 | 29 | empty |
| 4 | 53 | 0.30 | 0.76 | 16 | empty |
| 5 | 53 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 299 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5KBQ · Pak1 in complex with bis-anilino pyrimidine inhibitor · 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 0.98
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 5KBQ · PDBe 5KBQ · UniProt Q13153
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