SMTL ID : 6xq1.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-tetramer

Ligands

14 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 7 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:I.77, B:A.41 Hydrogen bonds: A:A.2, A:N.93 Water bridges: A:R.79, D:T.158 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: V74.6 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: Q.5, K.20, S.92, N.93, Y.94 Chain D: K.155 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.20 Hydrogen bonds: A:K.91, A:N.93 Salt bridges: A:K.20 ACT.4: 6 residues within 4Å: Chain A: E.156, Q.157, T.158 Chain D: A.4, R.95, R.97 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:E.156 Hydrogen bonds: A:T.158, A:T.158, A:T.158 Water bridges: A:E.156, 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 7 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:I.77, A:A.41 Hydrogen bonds: B:A.2, B:N.93 Water bridges: B:R.79, C:T.158 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: V74.12 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:A.2 Salt bridges: B:R.79, A:K.33 Hydrophobic interactions: A:K.33, A:V.44 ACT.9: 6 residues within 4Å: Chain B: Q.5, K.20, S.92, N.93, Y.94 Chain C: K.155 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.20 Hydrogen bonds: B:K.91, B:N.93 Salt bridges: B:K.20 ACT.10: 6 residues within 4Å: Chain B: E.156, Q.157, T.158 Chain C: A.4, R.95, R.97 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Water bridges: C:R.97, B:E.156 Salt bridges: C:R.97 Hydrophobic interactions: B:E.156 Hydrogen bonds: B:T.158, 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.14: 5 residues within 4Å: Chain C: A.2, R.79 Chain D: K.33, W.42 Ligands: V74.17 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:A.2 Salt bridges: C:R.79, D:K.33 ACT.15: 6 residues within 4Å: Chain B: K.155 Chain C: Q.5, K.20, S.92, N.93, Y.94 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.93, C:N.93 Salt bridges: C:K.20, B:K.155 ACT.18: 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 ACT.19: 5 residues within 4Å: Chain C: K.33, W.42 Chain D: A.2, R.79 Ligands: V74.22 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:A.2 Salt bridges: D:R.79, C:K.33 ACT.20: 6 residues within 4Å: Chain A: K.155 Chain D: Q.5, K.20, S.92, N.93, Y.94 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.93, D:N.93 Salt bridges: D:K.20, A:K.155

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

CL.5: 4 residues within 4Å: Chain A: T.39, E.40 Chain C: R.159, R.160 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: T.39, E.40 Chain D: R.159, R.160 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: R.159, R.160 Chain C: T.39, E.40 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: R.159, R.160 Chain D: T.39, E.40 Ligand excluded by PLIP

4 x V74: 3-[3-({[3-(4-carboxyphenoxy)phenyl]methoxy}methyl)phenyl]-1H-indole-2-carboxylic acid(Non-covalent)

V74.6: 13 residues within 4Å: Chain A: R.29, L.30, E.31, K.33, R.79, C.80, Q.81, E.89, K.91, S.92 Chain B: K.33 Ligands: ACT.2, V74.12 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.29, A:R.29, A:K.33, A:Q.81, A:Q.81, A:K.91, A:K.91, A:K.91 Hydrogen bonds: A:R.79, A:Q.81, A:K.91 Salt bridges: A:K.33, A:K.91, B:K.33 pi-Cation interactions: A:K.33, A:R.79, A:K.91 V74.12: 13 residues within 4Å: Chain A: K.33 Chain B: R.29, L.30, E.31, K.33, R.79, C.80, Q.81, E.89, K.91, S.92 Ligands: V74.6, ACT.8 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.29, B:R.29, B:K.33, B:Q.81, B:Q.81, B:K.91, B:K.91, B:K.91 Hydrogen bonds: B:R.79, B:Q.81, B:K.91 Salt bridges: B:K.33, B:K.91, A:K.33 pi-Cation interactions: B:K.33, B:R.79, B:K.91 V74.17: 11 residues within 4Å: Chain C: R.29, L.30, E.31, K.33, R.79, C.80, Q.81, K.91, S.92 Ligands: ACT.14, V74.22 16 PLIP interactions: 1 interactions with chain D, 15 interactions with chain C Salt bridges: D:K.33, C:K.33, C:K.91 Hydrophobic interactions: C:R.29, C:K.33, C:K.33, C:Q.81, C:Q.81, C:K.91, C:K.91, C:K.91 Hydrogen bonds: C:Q.81 Water bridges: C:K.91 pi-Cation interactions: C:K.33, C:R.79, C:K.91 V74.22: 11 residues within 4Å: Chain D: R.29, L.30, E.31, K.33, R.79, C.80, Q.81, K.91, S.92 Ligands: V74.17, ACT.19 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:R.29, D:K.33, D:K.33, D:Q.81, D:Q.81, D:K.91, D:K.91, D:K.91 Hydrogen bonds: D:Q.81 Water bridges: D:K.91 Salt bridges: D:K.33, D:K.91, C:K.33 pi-Cation interactions: D:K.33, D:R.79, D:K.91

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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