SMTL ID : 7lml.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 2.15 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: G.1, A.2, A.4, I.77, R.79, N.93 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: 2 residues within 4Å: Chain A: A.2, R.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.2 Salt bridges: A:R.79 ACT.3: 5 residues within 4Å: Chain A: Q.5, K.20, S.92, N.93, Y.94 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.5, A:Y.94 Hydrogen bonds: A:N.93 Salt bridges: A:K.20 ACT.9: 6 residues within 4Å: Chain B: G.1, A.2, A.4, I.77, R.79, N.93 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.4, B:I.77 Hydrogen bonds: B:A.2, B:N.93 Water bridges: B:G.1, B:G.1, B:R.79 Salt bridges: B:R.79 ACT.10: 2 residues within 4Å: Chain B: A.2, R.79 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.2 Salt bridges: B:R.79 ACT.11: 5 residues within 4Å: Chain B: Q.5, K.20, S.92, N.93, Y.94 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.20 Hydrogen bonds: B:Q.5, B:N.93 Salt bridges: B:K.20

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

CL.4: 2 residues within 4Å: Chain A: T.39, E.40 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: T.39, E.40 Ligand excluded by PLIP

8 x Y6S: 6-iodanyl-1~{H}-indole-2-carboxylic acid(Non-covalent)

Y6S.5: 5 residues within 4Å: Chain A: R.29, L.30, E.31, Q.81, E.89 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.29, A:E.31 Y6S.6: 7 residues within 4Å: Chain A: V.59, L.60, P.61, F.66 Chain B: P.68 Ligands: Y6S.7, Y6S.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.68, A:P.61 Y6S.7: 7 residues within 4Å: Chain A: D.54, S.55, R.58, P.68 Chain B: R.58 Ligands: Y6S.6, Y6S.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.58, A:R.58 Hydrophobic interactions: A:P.68 Y6S.8: 9 residues within 4Å: Chain A: E.31, W.32, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.33, A:R.79 Hydrogen bonds: A:C.80, A:Q.81, A:Q.81 Salt bridges: A:K.33 pi-Cation interactions: A:K.91 Y6S.13: 7 residues within 4Å: Chain A: P.68 Chain B: P.26, V.59, L.60, P.61 Ligands: Y6S.7, Y6S.15 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.60, B:P.61, A:P.68 Hydrogen bonds: B:V.59 Y6S.14: 5 residues within 4Å: Chain B: R.29, L.30, E.31, Q.81, E.89 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.31, B:Q.81 Y6S.15: 7 residues within 4Å: Chain A: R.58 Chain B: D.54, S.55, R.58, P.68 Ligands: Y6S.6, Y6S.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.68 Hydrogen bonds: A:R.58 Salt bridges: A:R.58 Y6S.16: 8 residues within 4Å: Chain B: E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:K.33, B:R.79, B:Q.81, B:K.91, B:K.91, B:K.91 Hydrogen bonds: B:E.31, B:E.31, B:K.91 Salt bridges: B:K.33 pi-Cation interactions: B:K.33

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

2021-12-15

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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