Research workbench
Structure of human cytochrome P450 1A1 with duocarmycin prodrug (S) ict-2726
Analyse Structure of human cytochrome P450 1A1 with duocarmycin prodrug (S) ict-2726 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UDM
- Type
- protein
- Length
- 1,876 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, Q4P, CPS
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 53% 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 | 467 | 54% helix, 10% strand | P04798 |
| B | Cytochrome P450 1A1 (EC 1.14.14.1, 4.2.1.152) | protein | 476 | 52% helix, 10% strand | P04798 |
| C | Cytochrome P450 1A1 (EC 1.14.14.1, 4.2.1.152) | protein | 468 | 53% helix, 10% strand | P04798 |
| D | Cytochrome P450 1A1 (EC 1.14.14.1, 4.2.1.152) | protein | 465 | 52% helix, 11% strand | P04798 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- Q4P · [(8S)-8-(chloromethyl)-7,8-dihydro-6H-furo[3,2-e]indol-6-yl](5-fluoro-1H-indol-2-yl)methanone · ligand · 4 copies · chains A, B, C, D
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.87 | 0.93 | 57 | HEM, Q4P |
| 2 | 556 | 0.87 | 0.93 | 57 | HEM, Q4P |
| 3 | 532 | 0.87 | 0.93 | 59 | HEM, Q4P |
| 4 | 522 | 0.87 | 0.93 | 58 | HEM, Q4P |
| 5 | 106 | 0.49 | 0.81 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 470 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 460 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 351 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 342 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6UDM · Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) ICT-2726 · 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 A 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 6UDM · PDBe 6UDM · UniProt P04798
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