MolNFT v1 · #76479 · protein
Human cytochrome P450 (cyp) 2D6 - prinomastat complex
3QM4 · Cytochrome P450 2D6: “Human cytochrome P450 (cyp) 2D6 - prinomastat complex”. X-ray diffraction, 3 ligands (HEM, PN0, NI), 10 pockets (best druggability 0.90). MolNFT v1 #76479 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3QM4
- Type
- protein
- Length
- 922 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2D6
- EC
- 1.14.14.1
- UniProt
- P10635
- Ligands
- HEM, PN0, NI
- Pockets
- 10 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 465 | 49% helix, 9% strand | P10635 |
| B | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 457 | 49% helix, 9% strand | P10635 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PN0 · Prinomastat · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.90 | 0.93 | 85 | HEM, PN0 |
| 2 | 561 | 0.87 | 0.93 | 63 | HEM, PN0 |
| 3 | 306 | 0.80 | 0.90 | 32 | empty |
| 4 | 823 | 0.72 | 0.77 | 68 | empty |
| 5 | 51 | 0.61 | 0.93 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1150 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 P10635
- Elsewhere: RCSB PDB 3QM4 · PDBe 3QM4 · UniProt P10635
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