MolNFT v1 · #102040 · protein
Crystal structure of retinol-binding protein 4 (RBP4)IN complex with a non-retinoid ligand
4O9S: “Crystal structure of retinol-binding protein 4 (RBP4)IN complex with a non-retinoid ligand”. X-ray diffraction, 2 ligands (2RY, CL), 5 pockets (best druggability 0.77). MolNFT v1 #102040 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4O9S
- Type
- protein
- Length
- 349 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 4
- UniProt
- P02753
- Ligands
- 2RY, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinol-binding protein 4 | protein | 175 | 10% helix, 47% strand | P02753 |
| B | Retinol-binding protein 4 | protein | 174 | 11% helix, 49% strand | P02753 |
Ligands and binding sites
- 2RY · 1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.77 | 0.89 | 32 | 2RY |
| 2 | 263 | 0.76 | 0.88 | 34 | 2RY |
| 3 | 510 | 0.65 | 0.77 | 49 | EDO |
| 4 | 56 | 0.28 | 0.74 | 13 | empty |
| 5 | 54 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 271 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4O9S · Crystal structure of Retinol-Binding Protein 4 (RBP4)in complex with a non-retinoid ligand · the same entry in another collection · chain A against A, TM-score 1.00
- P02753 · AlphaFold monomer V2.0 prediction for retinol-binding protein 4 (P02753) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P02753
- Elsewhere: RCSB PDB 4O9S · PDBe 4O9S · UniProt P02753
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