Research workbench
Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1T in P1 spacegroup
Analyse Crystal structure of the CXCR4 chemokine receptor in complex with a small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OE8
- Type
- protein
- Length
- 1,287 residues
- Chains
- 3
- 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
- ITD
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 72% 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 | 433 | 71% helix, 6% strand | P61073, P00720 |
| B | C-X-C chemokine receptor type 4, lysozyme chimera (EC 3.2.1.17) | protein | 426 | 72% helix, 5% strand | P61073, P00720 |
| C | C-X-C chemokine receptor type 4, lysozyme chimera (EC 3.2.1.17) | protein | 428 | 72% helix, 4% strand | P61073, P00720 |
Ligands and binding sites
- ITD · (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.77 | 0.80 | 70 | empty |
| 2 | 1012 | 0.75 | 0.77 | 65 | empty |
| 3 | 481 | 0.75 | 0.83 | 51 | ITD |
| 4 | 656 | 0.74 | 0.80 | 51 | ITD |
| 5 | 640 | 0.72 | 0.79 | 45 | ITD |
Interfaces
2 interfaces between chains.
- A–B · 968 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 712 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3OE8 · Crystal structure of the CXCR4 chemokine receptor in complex with a 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 A against A, TM-score 0.62
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 3OE8 · PDBe 3OE8 · UniProt P61073 · UniProt P00720
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