MolNFT v1 · #166022 · protein
Structure of human cytochrome P450 1A1 with duocarmycin prodrug (S) ict-2700
6UDL: “Structure of human cytochrome P450 1A1 with duocarmycin prodrug (S) ict-2700”. X-ray diffraction, 2 ligands (HEM, Q4M), 20 pockets (best druggability 0.88). MolNFT v1 #166022 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6UDL
- Type
- protein
- Length
- 1,877 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 1A1
- EC
- 1.14.14.1, 4.2.1.152
- UniProt
- P04798
- Ligands
- HEM, Q4M
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 1A1 (EC 1.14.14.1, 4.2.1.152) | protein | 469 | 52% helix, 10% strand | P04798 |
| B | Cytochrome P450 1A1 (EC 1.14.14.1, 4.2.1.152) | protein | 477 | 52% helix, 10% strand | P04798 |
| C | Cytochrome P450 1A1 (EC 1.14.14.1, 4.2.1.152) | protein | 466 | 51% helix, 10% strand | P04798 |
| D | Cytochrome P450 1A1 (EC 1.14.14.1, 4.2.1.152) | protein | 465 | 49% helix, 10% strand | P04798 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- Q4M · [(1S)-1-(chloromethyl)-1,6-dihydropyrrolo[3,2-e]indol-3(2H)-yl](5-methoxy-1H-indol-2-yl)methanone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.88 | 0.93 | 61 | HEM |
| 2 | 562 | 0.87 | 0.92 | 61 | HEM |
| 3 | 540 | 0.87 | 0.92 | 54 | HEM, Q4M |
| 4 | 511 | 0.86 | 0.92 | 52 | HEM, Q4M |
| 5 | 633 | 0.67 | 0.76 | 77 | empty |
Interfaces
3 interfaces between chains.
- A–B · 584 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 525 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 355 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6UDL · Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) ICT-2700 · the same entry in another collection · chain D against D, TM-score 1.00
- P04798 · AlphaFold monomer V2.0 prediction for cytochrome P450 1A1 (P04798) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P04798
- Elsewhere: RCSB PDB 6UDL · PDBe 6UDL · UniProt P04798
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