SMTL ID : 4psq.1 (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 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.41, A:K.41, A:R.48, A:R.48 Salt bridges: A:K.41, A:R.48

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

EDO.3: 5 residues within 4Å: Chain A: F.38, R.39, V.136, R.184, E.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.39 EDO.4: 3 residues within 4Å: Chain A: S.36, K.114, W.134 No protein-ligand interaction detected (PLIP) EDO.5: 7 residues within 4Å: Chain A: R.182, Q.185, L.190, A.191, R.192, Q.193, Y.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.192, A:Q.193, A:Y.194 EDO.6: 3 residues within 4Å: Chain A: D.132, C.149, R.150 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: Y.140, D.141, R.168 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain A: Y.194, R.195, L.196 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.194, A:L.196 Water bridges: A:R.195, A:L.196 EDO.9: 2 residues within 4Å: Chain A: R.34, D.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.34, A:D.155 EDO.10: 6 residues within 4Å: Chain A: D.137, T.138, D.139, Y.143, I.180, R.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.138, A:R.184

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
B

Retinol-binding protein 4

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