Research workbench
CYP2C8DH complexed with 2 molecules of 9-cis retinoic acid
Analyse CYP2C8DH complexed with 2 molecules of 9-cis retinoic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NNH
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2C8
- EC
- 1.14.14.1
- UniProt
- P10632
- Ligands
- 9CR, HEM, PLM, SO4
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome P450 2C8 (EC 1.14.14.1) | protein | 463 | 52% helix, 9% strand | P10632 |
Ligands and binding sites
- 9CR · (9cis)-retinoic acid · ligand · 4 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
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 | 1171 | 0.86 | 0.87 | 112 | HEM, 9CR |
| 2 | 1109 | 0.86 | 0.86 | 98 | HEM, 9CR |
| 3 | 1176 | 0.80 | 0.81 | 103 | PLM |
| 4 | 186 | 0.47 | 0.75 | 22 | empty |
| 5 | 55 | 0.36 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 274 Ų buried · 2 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 P10632
- Elsewhere: RCSB PDB 2NNH · PDBe 2NNH · UniProt P10632
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