SMTL ID : 7lmw.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 2.50 Å

Oligo State

homo-dimer

Ligands

6 x Y6P: 7-methyl-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic acid(Non-covalent)

Y6P.1: 10 residues within 4Å: Chain A: A.2, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: ACT.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.2, A:R.79, A:Q.81, A:K.91, A:K.91, A:K.91, A:N.93 Hydrogen bonds: A:E.31 Salt bridges: A:K.33, A:K.91 pi-Cation interactions: A:K.33, A:K.91 Y6P.2: 5 residues within 4Å: Chain A: K.43, G.50, G.51, P.52, W.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.43 Y6P.5: 9 residues within 4Å: Chain A: D.54, S.55, R.58, F.66, P.68 Chain B: R.58, V.59, L.60 Ligands: Y6P.7 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:R.58, B:L.60, A:P.68 Hydrogen bonds: B:R.58 pi-Cation interactions: B:R.58, A:R.58 Salt bridges: A:R.58 Y6P.6: 9 residues within 4Å: Chain B: A.2, E.31, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: ACT.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.2, B:R.79, B:Q.81, B:K.91, B:K.91, B:K.91, B:N.93 Hydrogen bonds: B:E.31, B:E.31 Salt bridges: B:K.91 pi-Cation interactions: B:K.91 Y6P.7: 8 residues within 4Å: Chain A: R.58, V.59, L.60 Chain B: D.54, S.55, R.58, P.68 Ligands: Y6P.5 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.54, B:D.54, A:R.58, A:V.59 Salt bridges: B:R.58 pi-Cation interactions: A:R.58 Y6P.8: 5 residues within 4Å: Chain B: K.43, G.50, G.51, P.52, W.53 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.52 Hydrogen bonds: B:K.43, B:K.43 Water bridges: B:G.50 Salt bridges: B:K.43

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

ACT.3: 3 residues within 4Å: Chain A: A.2, R.79 Ligands: Y6P.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.2 Salt bridges: A:R.79 ACT.4: 6 residues within 4Å: Chain A: G.1, A.2, A.4, I.77, R.79, N.93 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.4 Hydrogen bonds: A:A.2, A:N.93, A:N.93 Water bridges: A:R.79, A:R.79 Salt bridges: A:R.79 ACT.10: 4 residues within 4Å: Chain B: A.2, R.79 Ligands: Y6P.6, ACT.11 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.79 ACT.11: 6 residues within 4Å: Chain B: G.1, W.42, I.77, R.79 Ligands: ACT.10, ACT.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.42, B:I.77 Hydrogen bonds: B:A.2 Salt bridges: B:R.79 ACT.12: 7 residues within 4Å: Chain B: G.1, A.2, A.4, I.77, R.79, N.93 Ligands: ACT.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.2 Hydrogen bonds: B:A.2, B:N.93 Water bridges: B:G.1

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

CL.9: 2 residues within 4Å: Chain B: R.159, R.160 Ligand excluded by PLIP

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

2021-07-28

Peptides

Advanced glycosylation end product-specific receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Advanced glycosylation end product-specific receptor

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