SMTL ID : 3oe6.1

Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in I222 spacegroup

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 x ITD: (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate(Non-covalent)

ITD.1: 12 residues within 4Å: Chain A: W.104, D.107, A.108, W.112, V.122, H.123, Y.126, R.193, I.195, C.196, D.197, E.462 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.104, A:W.104, A:W.104, A:W.112, A:V.122, A:Y.126, A:Y.126, A:I.195 Hydrogen bonds: A:D.107 ITD.6: 12 residues within 4Å: Chain B: W.104, D.107, A.108, W.112, V.122, H.123, Y.126, R.193, I.195, C.196, D.197, E.462 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.104, B:W.104, B:W.104, B:W.112, B:V.122, B:Y.126, B:Y.126, B:I.195 Hydrogen bonds: B:D.107

6 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 9 residues within 4Å: Chain A: G.65, L.68, V.69, V.72, M.73, P.473, Y.476, A.477, L.479 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.68, A:V.69, A:Y.476, A:A.477 OLC.3: 3 residues within 4Å: Chain A: V.109, A.110, Y.113 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.109, A:A.110 OLC.4: 5 residues within 4Å: Chain A: K.48, I.49, P.52, T.53, S.56 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.52 OLC.7: 9 residues within 4Å: Chain B: G.65, L.68, V.69, V.72, M.73, P.473, Y.476, A.477, L.479 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.68, B:V.69, B:Y.476, B:A.477 OLC.8: 3 residues within 4Å: Chain B: V.109, A.110, Y.113 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.109, B:A.110 OLC.9: 5 residues within 4Å: Chain B: K.48, I.49, P.52, T.53, S.56 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.52

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: L.130, S.133, V.134, H.213, G.217, F.422, W.426, Y.430 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.133, A:H.213 GOL.10: 8 residues within 4Å: Chain B: L.130, S.133, V.134, H.213, G.217, F.422, W.426, Y.430 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.133, B:H.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, B. et al., Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science (2010)

Release Date

2010-10-27

Peptides

C-X-C chemokine receptor type 4, Lysozyme Chimera: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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C-X-C chemokine receptor type 4, Lysozyme Chimera