MolNFT v1 · #143375 · protein
Crebbp bromodomain in complex with CPD6 (methyl 1H-indole-3- carboxylate)
6AXQ · Creb-binding protein: “Crebbp bromodomain in complex with CPD6 (methyl 1H-indole-3- carboxylate)”. X-ray diffraction, 1 ligand (C2Y), 9 pockets (best druggability 0.79). MolNFT v1 #143375 on GenesisL1: 3D structure, binding sites…
- PDB
- 6AXQ
- Type
- protein
- Length
- 450 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Creb-binding protein
- EC
- 2.3.1.48
- UniProt
- Q92793
- Ligands
- C2Y
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Creb-binding protein (EC 2.3.1.48) | protein | 112 | 68% helix, 0% strand | Q92793 |
| D | Creb-binding protein (EC 2.3.1.48) | protein | 114 | 68% helix, 0% strand | Q92793 |
Ligands and binding sites
- C2Y · methyl 1H-indole-3-carboxylate · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.79 | 0.81 | 64 | DMS |
| 2 | 235 | 0.68 | 0.84 | 28 | DMS |
| 3 | 104 | 0.50 | 0.81 | 19 | C2Y |
| 4 | 101 | 0.50 | 0.81 | 19 | C2Y |
| 5 | 85 | 0.47 | 0.81 | 19 | C2Y |
Interfaces
4 interfaces between chains.
- B–D · 1104 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 465 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 335 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 148 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6AXQ · CREBBP bromodomain in complex with Cpd6 (methyl 1H-indole-3-carboxylate) · the same entry in another collection · chain D against D, TM-score 1.00
- Q92793 · AlphaFold monomer V2.0 prediction for creb-binding protein (Q92793) · 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 Q92793
- Elsewhere: RCSB PDB 6AXQ · PDBe 6AXQ · UniProt Q92793
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