Research workbench
The 2.5 a structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1T
Analyse The 2.5 a structure of the CXCR4 chemokine receptor in complex with small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ODU
- Type
- protein
- Length
- 922 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-X-C chemokine receptor type 4, lysozyme chimera
- EC
- 3.2.1.17
- UniProt
- P61073, P00720
- Ligands
- OLA, ITD
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-X-C chemokine receptor type 4, lysozyme chimera (EC 3.2.1.17) | protein | 466 | 70% helix, 5% strand | P61073, P00720 |
| B | C-X-C chemokine receptor type 4, lysozyme chimera (EC 3.2.1.17) | protein | 456 | 70% helix, 5% strand | P61073, P00720 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 6 copies · chains A, B
- ITD · (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate · ligand · 2 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.80 | 0.83 | 59 | ITD, OLC |
| 2 | 787 | 0.80 | 0.83 | 56 | ITD, OLA |
| 3 | 908 | 0.78 | 0.80 | 91 | empty |
| 4 | 536 | 0.66 | 0.77 | 40 | empty |
| 5 | 134 | 0.54 | 0.82 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1283 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3ODU · The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule… · the same entry in another collection · chain A against A, TM-score 1.00
- P61073 · AlphaFold monomer V2.0 prediction for C-X-C chemokine receptor type 4 (P61073) · a predicted model of the same protein · chain B against A, TM-score 0.60
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 P61073
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 3ODU · PDBe 3ODU · UniProt P61073 · UniProt P00720
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