SMTL ID : 4psq.2 (1 other biounit)

Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with a non-retinoid ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x 2WL: (1-benzyl-1H-imidazol-4-yl)[4-(2-chlorophenyl)piperazin-1-yl]methanone(Non-covalent)

2WL.1: 13 residues within 4Å: Chain A: L.64, F.65, L.66, A.86, M.102, V.103, G.104, M.117, Y.119, G.129, R.150, Y.162, F.164 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.86, A:Y.119 Hydrogen bonds: A:L.66, A:R.150, A:R.150 pi-Stacking: A:Y.119

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: K.41, R.48, Y.140 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.41, A:R.48, A:Y.140 Salt bridges: A:K.41, A:R.48

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: R.182, Q.185, L.190, A.191, R.192, Q.193, Y.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.192, A:Q.193, A:Y.194 Water bridges: A:Q.185 EDO.4: 4 residues within 4Å: Chain A: D.132, C.149, R.150, L.152 No protein-ligand interaction detected (PLIP) EDO.5: 7 residues within 4Å: Chain A: F.38, R.39, V.136, R.184, E.187, L.188 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.39 EDO.6: 2 residues within 4Å: Chain A: R.34, D.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.155 EDO.7: 5 residues within 4Å: Chain A: R.192, Q.193, Y.194, R.195 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.192 EDO.8: 4 residues within 4Å: Chain A: W.96, D.97, V.98, C.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.99, A:C.99 EDO.9: 4 residues within 4Å: Chain A: C.158, S.161, L.190, Q.193 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.161, A:S.161, A:Q.193 Water bridges: A:K.59, A:C.158, A:S.161 EDO.10: 1 residues within 4Å: Chain A: K.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.128 EDO.11: 3 residues within 4Å: Chain A: S.36, K.114, W.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.114 EDO.12: 6 residues within 4Å: Chain A: K.58, K.59, D.60, Q.193, R.195 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.60, A:Q.193, A:R.195 EDO.13: 6 residues within 4Å: Chain A: R.39, V.40, V.136, D.137, R.184 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.184 Water bridges: A:V.40, A:E.42 EDO.14: 4 residues within 4Å: Chain A: V.71, T.85, A.86, K.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.85, A:T.85, A:K.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structure-assisted discovery of the first non-retinoid ligands for Retinol-Binding Protein 4. Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-07-02

Peptides

Retinol-binding protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Retinol-binding protein 4

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