MolNFT v1 · #112378 · protein
PAK1 in complex with (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro- dibenzodiazepin-11-YL)AMINO)PYRROLIDINE-1-carboxamide
4ZJJ · SERINE/THREONINE-protein kinase pak 1: “PAK1 in complex with (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro…”. X-ray diffraction, 2 ligands (4OR, MG), 11 pockets (best druggability 0.78). MolNFT v1 #112378 on GenesisL1: 3D…
- PDB
- 4ZJJ
- Type
- protein
- Length
- 1,107 residues
- Chains
- 4
- 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
- 4OR, MG
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 280 | 45% helix, 18% strand | Q13153 |
| B | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 277 | 43% helix, 18% strand | Q13153 |
| C | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 276 | 45% helix, 16% strand | Q13153 |
| D | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 274 | 43% helix, 15% strand | Q13153 |
Ligands and binding sites
- 4OR · (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.78 | 0.87 | 42 | 4OR |
| 2 | 423 | 0.77 | 0.86 | 46 | 4OR |
| 3 | 401 | 0.75 | 0.84 | 41 | 4OR |
| 4 | 879 | 0.74 | 0.78 | 92 | empty |
| 5 | 945 | 0.72 | 0.76 | 88 | MG |
Interfaces
6 interfaces between chains.
- B–C · 1246 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1201 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 339 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 300 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZJJ · PAK1 in complex with (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-y… · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.89
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 4ZJJ · PDBe 4ZJJ · UniProt Q13153
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