SMTL ID : 4o9s.3 (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

homo-dimer

Ligands

2 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: 21 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 Chain B: W.99 Ligands: CL.16 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.67, A:Y.122, A:Y.122, A:F.128, B:W.99 Hydrogen bonds: A:R.153 2RY.18: 22 residues within 4Å: Chain A: W.99 Chain B: 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 Ligands: EDO.13 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.67, B:A.87, B:A.89, B:Y.122, B:Y.122, B:F.128, A:W.99 Hydrogen bonds: B:R.153 Water bridges: B:R.153

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

EDO.2: 3 residues within 4Å: Chain A: E.113, D.114, P.115 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: F.41, R.42, V.139, R.187, E.190, L.191 Ligands: EDO.11 Ligand excluded by PLIP EDO.4: 1 residues within 4Å: Chain A: L.176 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: T.112, E.113, P.115 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: Q.188, A.194, R.195, Q.196, Y.197 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: V.74, T.88, A.89, K.90 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: K.61, D.63, Q.196, R.198 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: K.62, D.63, P.64, E.65, A.162, D.163, S.164 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: N.72, V.74, H.202, N.203, G.204 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: R.42, V.43, K.44, V.139, R.187 Ligands: EDO.3 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: P.173, N.174, H.202 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: L.96, N.98, W.99 Chain B: L.67 Ligands: 2RY.18 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain A: W.123 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: P.177, P.178, E.179 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: F.41, R.42, V.139, R.187, E.190, L.191 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: R.34, D.35, C.36, T.160 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: R.42, V.43, K.44, V.139, D.140, R.187 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: D.135, C.152, L.155 Ligands: EDO.27, EDO.31 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: K.62, D.63, Q.196, R.198 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: K.119, N.133, D.134, D.135 Ligands: EDO.30, EDO.31 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: W.123, G.124, L.129, Q.130, K.131 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: L.155 Ligands: EDO.23, EDO.31 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain B: Q.181, R.185 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: R.185, Q.188, R.195, Q.196, Y.197 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: N.133, D.134, D.135, R.153 Ligands: EDO.25 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: K.119, D.135 Ligands: EDO.23, EDO.25, EDO.27 Ligand excluded by PLIP

3 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: 2 residues within 4Å: Chain B: W.99 Ligands: 2RY.1 Ligand excluded by PLIP CL.32: 7 residues within 4Å: Chain B: A.103, D.104, G.124, V.125, A.126, S.127, F.128 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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Retinol-binding protein 4

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