MolNFT v1 · #181878 · protein
Human CYP11B2 in complex with LCI699
7M8V · Cytochrome P450 11B2, mitochondrial: “Human CYP11B2 in complex with LCI699”. X-ray diffraction, 2 ligands (YSY, HEM), 20 pockets (best druggability 0.88). MolNFT v1 #181878 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7M8V
- Type
- protein
- Length
- 5,545 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 11B2, mitochondrial
- EC
- 1.14.15.5, 1.14.15.4
- UniProt
- P19099
- Ligands
- YSY, HEM
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 11 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 464 | 57% helix, 9% strand | P19099 |
| B | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 462 | 56% helix, 10% strand | P19099 |
| C | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 465 | 56% helix, 10% strand | P19099 |
| D | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 463 | 56% helix, 10% strand | P19099 |
| E, F | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 461 | 57% helix, 10% strand | P19099 |
| G | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 461 | 58% helix, 10% strand | P19099 |
| H | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 464 | 58% helix, 10% strand | P19099 |
| I | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 462 | 57% helix, 10% strand | P19099 |
| J | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 459 | 57% helix, 10% strand | P19099 |
| K | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 464 | 57% helix, 10% strand | P19099 |
| L | Cytochrome P450 11B2, mitochondrial (EC 1.14.15.5, 1.14.15.4) | protein | 459 | 58% helix, 10% strand | P19099 |
Ligands and binding sites
- YSY · 4-[(4R,5R)-6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-5-yl]-3-fluorobenzonitrile · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.88 | 0.89 | 93 | YSY, HEM |
| 2 | 859 | 0.88 | 0.90 | 89 | YSY, HEM |
| 3 | 950 | 0.87 | 0.88 | 91 | YSY, HEM |
| 4 | 871 | 0.87 | 0.89 | 90 | YSY, HEM |
| 5 | 974 | 0.87 | 0.88 | 92 | YSY, HEM |
Interfaces
17 interfaces between chains.
- A–D · 741 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 740 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 739 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 739 Ų buried · 14 hydrogen bonds · protein-protein
- G–L · 735 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7M8V · Human CYP11B2 in complex with LCI699 · the same entry in another collection · chain L against L, 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 P19099
- Elsewhere: RCSB PDB 7M8V · PDBe 7M8V · UniProt P19099
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