SMTL ID : 4o9s.2 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x 2RY: 1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone(Non-covalent)

2RY.1: 20 residues within 4Å: Chain A: L.67, F.68, L.69, F.77, A.87, T.88, A.89, V.93, M.105, V.106, G.107, M.120, Y.122, F.128, D.134, H.136, R.153, Y.165, F.167, F.169 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.67, A:A.87, A:A.89, A:Y.122, A:Y.122, A:F.128 Hydrogen bonds: A:R.153 Water bridges: A:R.153

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

EDO.2: 3 residues within 4Å: Chain A: P.177, P.178, E.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.179 Water bridges: A:D.142, A:T.145 EDO.3: 6 residues within 4Å: Chain A: F.41, R.42, V.139, R.187, E.190, L.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.42, A:R.42 EDO.4: 4 residues within 4Å: Chain A: R.34, D.35, C.36, T.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.36 EDO.5: 6 residues within 4Å: Chain A: R.42, V.43, K.44, V.139, D.140, R.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.43 Water bridges: A:E.45 EDO.6: 5 residues within 4Å: Chain A: D.135, C.152, L.155 Ligands: EDO.10, EDO.14 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: K.62, D.63, Q.196, R.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.63, A:D.63, A:R.198 EDO.8: 6 residues within 4Å: Chain A: K.119, N.133, D.134, D.135 Ligands: EDO.13, EDO.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.133, A:D.135 EDO.9: 5 residues within 4Å: Chain A: W.123, G.124, L.129, Q.130, K.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.124 Water bridges: A:G.124 EDO.10: 3 residues within 4Å: Chain A: L.155 Ligands: EDO.6, EDO.14 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain A: Q.181, R.185 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: R.185, Q.188, R.195, Q.196, Y.197 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.185, A:Q.188, A:R.195, A:Q.196, A:Y.197, A:Y.197 EDO.13: 5 residues within 4Å: Chain A: N.133, D.134, D.135, R.153 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.134, A:D.135, A:D.135 Water bridges: A:D.135 EDO.14: 5 residues within 4Å: Chain A: K.119, D.135 Ligands: EDO.6, EDO.8, EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.119, A:D.135

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 7 residues within 4Å: Chain A: A.103, D.104, G.124, V.125, A.126, S.127, F.128 Ligand excluded by PLIP

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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