SMTL ID : 4o9s.1 (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, 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 Ligands: CL.16 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.67, A:Y.122, A:Y.122, A:F.128 Hydrogen bonds: A:R.153

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

EDO.2: 3 residues within 4Å: Chain A: E.113, D.114, P.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.113, A:E.113, A:D.114 EDO.3: 7 residues within 4Å: Chain A: F.41, R.42, V.139, R.187, E.190, L.191 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.42, A:E.190 EDO.4: 1 residues within 4Å: Chain A: L.176 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: T.112, E.113, P.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.112 EDO.6: 5 residues within 4Å: Chain A: Q.188, A.194, R.195, Q.196, Y.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.195, A:Q.196, A:Y.197 Water bridges: A:Y.197 EDO.7: 4 residues within 4Å: Chain A: V.74, T.88, A.89, K.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.88, A:T.88, A:K.90 EDO.8: 4 residues within 4Å: Chain A: K.61, D.63, Q.196, R.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.63, A:Q.196 EDO.9: 7 residues within 4Å: Chain A: K.62, D.63, P.64, E.65, A.162, D.163, S.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.62, A:S.164, A:S.164 EDO.10: 5 residues within 4Å: Chain A: N.72, V.74, H.202, N.203, G.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.72, A:H.202, A:G.204 EDO.11: 6 residues within 4Å: Chain A: R.42, V.43, K.44, V.139, R.187 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.139, A:R.187 Water bridges: A:E.45 EDO.12: 3 residues within 4Å: Chain A: P.173, N.174, H.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.174, A:H.202 EDO.13: 3 residues within 4Å: Chain A: L.96, N.98, W.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.98, A:W.99 EDO.14: 1 residues within 4Å: Chain A: W.123 No protein-ligand interaction detected (PLIP)

2 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 CL.16: 1 residues within 4Å: Ligands: 2RY.1 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 3 residues within 4Å: Chain A: D.135, C.152, L.155 No protein-ligand interaction detected (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
A

Retinol-binding protein 4

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