SMTL ID : 6xq3.1

Receptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-(((3-(4-Carboxyphenoxy)benzyl)oxy)methyl)phenyl)-1H-indole-2-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-tetramer

Ligands

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: G.1, A.2, A.4, I.77, R.79, N.93 Chain B: A.41 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.4, A:I.77 Hydrogen bonds: A:A.2, A:N.93, A:N.93 Water bridges: A:G.1, A:R.79, A:R.79 Salt bridges: A:R.79 ACT.2: 6 residues within 4Å: Chain A: A.2, R.79 Chain B: K.33, W.42, V.44 Ligands: V6Y.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.33, B:V.44 Salt bridges: B:K.33, A:R.79 Water bridges: A:A.2 ACT.3: 6 residues within 4Å: Chain A: E.156, Q.157, T.158 Chain D: A.4, R.95, R.97 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:E.156, D:A.4, D:R.95 Hydrogen bonds: A:T.158, A:T.158 Water bridges: A:E.156, A:E.156, D:R.97, D:R.97 Salt bridges: D:R.97 ACT.7: 7 residues within 4Å: Chain A: A.41 Chain B: G.1, A.2, A.4, I.77, R.79, N.93 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.4, B:I.77 Hydrogen bonds: B:A.2, B:N.93, B:N.93 Water bridges: B:G.1, B:R.79, B:R.79 Salt bridges: B:R.79 ACT.8: 6 residues within 4Å: Chain A: K.33, W.42, V.44 Chain B: A.2, R.79 Ligands: V6Y.11 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.33, A:V.44 Salt bridges: A:K.33, B:R.79 Water bridges: B:A.2 ACT.9: 6 residues within 4Å: Chain B: E.156, Q.157, T.158 Chain C: A.4, R.95, R.97 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:A.4, C:R.95, B:E.156 Water bridges: C:R.97, C:R.97, B:E.156, B:E.156 Salt bridges: C:R.97 Hydrogen bonds: B:T.158, B:T.158 ACT.13: 7 residues within 4Å: Chain C: G.1, A.2, A.4, I.77, R.79, N.93 Chain D: A.41 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.4, C:I.77 Hydrogen bonds: C:A.2, C:N.93 Water bridges: C:G.1, C:R.79, C:R.79 Salt bridges: C:R.79 ACT.17: 7 residues within 4Å: Chain C: A.41 Chain D: G.1, A.2, A.4, I.77, R.79, N.93 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.4, D:I.77 Hydrogen bonds: D:A.2, D:N.93 Water bridges: D:G.1, D:R.79, D:R.79 Salt bridges: D:R.79

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

CL.4: 4 residues within 4Å: Chain A: T.39, E.40 Chain C: R.159, R.160 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: T.39, E.40 Chain D: R.159, R.160 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: R.159, R.160 Chain C: T.39, E.40 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: R.159, R.160 Chain D: T.39, E.40 Ligand excluded by PLIP

8 x V6Y: 3-(3-{[3-(4-carboxyphenoxy)phenyl]methoxy}phenyl)-1H-indole-2-carboxylic acid(Non-covalent)

V6Y.5: 15 residues within 4Å: Chain A: A.2, M.3, A.4, K.20, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Chain D: K.155 Ligands: ACT.2, V6Y.11 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:A.2, A:M.3, A:E.31, A:K.33, A:R.79, A:Q.81, A:K.91, A:K.91, A:K.91, D:K.155 Hydrogen bonds: A:K.91, A:N.93 Salt bridges: A:K.20, A:K.91, D:K.155 pi-Cation interactions: A:K.33, A:K.33 V6Y.6: 11 residues within 4Å: Chain A: P.26, P.47, Q.48, D.54, S.55, R.58, V.59, L.60, P.61, F.66, P.68 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.47, A:Q.48, A:R.58, A:R.58, A:L.60, A:F.66, A:P.68 Hydrogen bonds: A:S.55, A:R.58 Water bridges: A:Q.28, A:Q.28 pi-Cation interactions: A:R.58 V6Y.11: 15 residues within 4Å: Chain B: A.2, M.3, A.4, K.20, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Chain C: K.155 Ligands: V6Y.5, ACT.8 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.2, B:M.3, B:E.31, B:K.33, B:R.79, B:Q.81, B:K.91, B:K.91, B:K.91, C:K.155 Hydrogen bonds: B:K.91, B:N.93 Salt bridges: B:K.20, B:K.91, C:K.155 pi-Cation interactions: B:K.33, B:K.33 V6Y.12: 11 residues within 4Å: Chain B: P.26, P.47, Q.48, D.54, S.55, R.58, V.59, L.60, P.61, F.66, P.68 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.47, B:Q.48, B:R.58, B:R.58, B:L.60, B:F.66, B:P.68 Hydrogen bonds: B:S.55, B:R.58 Water bridges: B:Q.28, B:Q.28 pi-Cation interactions: B:R.58 V6Y.15: 14 residues within 4Å: Chain B: K.155 Chain C: A.2, M.3, A.4, K.20, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: V6Y.19 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.2, C:M.3, C:E.31, C:K.33, C:R.79, C:Q.81, C:K.91, C:K.91, C:K.91, C:N.93, B:K.155 Hydrogen bonds: C:N.93 Salt bridges: C:K.20, C:K.91, B:K.155 pi-Cation interactions: C:K.33, C:K.33, C:K.91 V6Y.16: 8 residues within 4Å: Chain C: D.54, S.55, R.58, V.59, L.60, P.61, F.66, P.68 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:R.58, C:L.60, C:P.61, C:F.66, C:P.68 V6Y.19: 14 residues within 4Å: Chain A: K.155 Chain D: A.2, M.3, A.4, K.20, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: V6Y.15 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:A.2, D:M.3, D:E.31, D:K.33, D:R.79, D:Q.81, D:K.91, D:K.91, D:K.91, D:N.93, A:K.155 Hydrogen bonds: D:N.93 Salt bridges: D:K.20, D:K.91, A:K.155 pi-Cation interactions: D:K.33, D:K.33, D:K.91 V6Y.20: 8 residues within 4Å: Chain D: D.54, S.55, R.58, V.59, L.60, P.61, F.66, P.68 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:R.58, D:L.60, D:P.61, D:F.66, D:P.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kozlyuk, N. et al., A fragment-based approach to discovery of Receptor for Advanced Glycation End products inhibitors. Proteins (2021)

Release Date

2021-07-14

Peptides

Advanced glycosylation end product-specific receptor: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Advanced glycosylation end product-specific receptor

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