SMTL ID : 3odu.1

The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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: 13 residues within 4Å: Chain A: E.42, W.104, D.107, W.112, V.122, Y.126, R.193, I.195, C.196, D.197, R.198, E.462 Ligands: OLC.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.104, A:W.112, A:V.122, A:I.195 Hydrogen bonds: A:D.107 ITD.6: 12 residues within 4Å: Chain B: E.42, W.104, D.107, W.112, V.122, Y.126, R.193, I.195, C.196, D.197, R.198, E.462 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.112, B:V.122, B:I.195 Hydrogen bonds: B:D.107

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

OLC.2: 3 residues within 4Å: Chain A: F.114, F.117, L.118 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.118 OLC.3: 13 residues within 4Å: Chain A: V.207, Q.210, F.211, I.214, I.219, I.433, D.436, S.437, L.440, H.455, I.458 Chain B: V.208 Ligands: ITD.1 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:V.208, A:V.207, A:Q.210, A:F.211, A:F.211, A:I.214, A:I.214, A:I.219, A:D.436 Hydrogen bonds: A:H.455 OLC.4: 11 residues within 4Å: Chain A: L.130, V.134, H.213, I.214, G.217, L.218, I.219, F.422, Y.430, I.433, S.434 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.219, A:Y.430, A:Y.430, A:I.433 Hydrogen bonds: A:L.130, A:G.217 OLC.7: 9 residues within 4Å: Chain B: T.61, L.68, V.69, V.72, C.470, P.473, I.474, Y.476, A.477 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.68, B:P.473, B:I.474 OLC.8: 1 residues within 4Å: Chain B: I.444 No protein-ligand interaction detected (PLIP)

6 x OLA: OLEIC ACID(Non-covalent)

OLA.5: 4 residues within 4Å: Chain A: V.106, V.109, A.110, Y.113 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.106, A:V.109, A:A.110 Hydrogen bonds: A:Y.113 OLA.9: 9 residues within 4Å: Chain B: I.49, P.52, T.53, S.56, A.105, V.106, V.109, A.110, Y.113 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.49, B:P.52, B:A.105, B:V.106, B:V.109, B:A.110, B:Y.113 OLA.10: 9 residues within 4Å: Chain A: V.208 Chain B: V.206, Q.210, F.211, I.214, I.219, D.436, S.437, L.440 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.208, A:V.208, B:V.206, B:Q.210, B:F.211, B:I.214, B:I.219, B:L.440 OLA.11: 8 residues within 4Å: Chain B: R.80, L.88, H.89, V.92, L.96, Y.167, W.171, L.175 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.88, B:V.92, B:L.96, B:Y.167, B:W.171, B:W.171, B:L.175 Hydrogen bonds: B:Y.167 Salt bridges: B:R.80, B:H.89 OLA.12: 4 residues within 4Å: Chain B: A.421, A.424, C.425, L.464 No protein-ligand interaction detected (PLIP) OLA.13: 7 residues within 4Å: Chain B: L.130, I.214, L.218, F.422, W.426, Y.430, S.434 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.130, B:L.218, B:W.426, B:Y.430, B:Y.430 Hydrogen bonds: B:Y.430 Water bridges: B:S.133

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
B

Membrane

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

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