SMTL ID : 6xq7.1

Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

18 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 Ligand excluded by PLIP ACT.2: 7 residues within 4Å: Chain A: Q.5, K.20, K.91, S.92, N.93, Y.94 Chain D: K.155 Ligand excluded by PLIP ACT.3: 6 residues within 4Å: Chain A: A.2, R.79 Chain B: K.33, W.42, V.44 Ligands: V6V.10 Ligand excluded by PLIP ACT.4: 5 residues within 4Å: Chain A: L.114, V.175, P.177, P.185, F.187 Ligand excluded by PLIP ACT.12: 7 residues within 4Å: Chain A: A.41 Chain B: G.1, A.2, A.4, I.77, R.79, N.93 Ligand excluded by PLIP ACT.13: 7 residues within 4Å: Chain B: Q.5, K.20, K.91, S.92, N.93, Y.94 Chain C: K.155 Ligand excluded by PLIP ACT.14: 6 residues within 4Å: Chain A: K.33, W.42, V.44 Chain B: A.2, R.79 Ligands: V6V.21 Ligand excluded by PLIP ACT.15: 5 residues within 4Å: Chain B: L.114, V.175, P.177, P.185, F.187 Ligand excluded by PLIP ACT.23: 7 residues within 4Å: Chain C: G.1, A.2, A.4, I.77, R.79, N.93 Chain D: A.41 Ligand excluded by PLIP ACT.24: 6 residues within 4Å: Chain B: K.155 Chain C: Q.5, K.20, S.92, N.93, Y.94 Ligand excluded by PLIP ACT.25: 5 residues within 4Å: Chain C: A.2, R.79 Chain D: K.33, W.42, V.44 Ligand excluded by PLIP ACT.26: 7 residues within 4Å: Chain C: D.54, S.55, V.56, A.57, R.58, F.66, P.68 Ligand excluded by PLIP ACT.27: 6 residues within 4Å: Chain C: I.101, F.191, P.193, H.198, R.199, L.201 Ligand excluded by PLIP ACT.30: 7 residues within 4Å: Chain C: A.41 Chain D: G.1, A.2, A.4, I.77, R.79, N.93 Ligand excluded by PLIP ACT.31: 6 residues within 4Å: Chain A: K.155 Chain D: Q.5, K.20, S.92, N.93, Y.94 Ligand excluded by PLIP ACT.32: 5 residues within 4Å: Chain C: K.33, W.42, V.44 Chain D: A.2, R.79 Ligand excluded by PLIP ACT.33: 7 residues within 4Å: Chain D: D.54, S.55, V.56, A.57, R.58, F.66, P.68 Ligand excluded by PLIP ACT.34: 6 residues within 4Å: Chain D: I.101, F.191, P.193, H.198, R.199, L.201 Ligand excluded by PLIP

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

CL.5: 4 residues within 4Å: Chain A: R.159, R.160 Chain C: T.39, E.40 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: T.39, E.40 Chain C: R.159, R.160 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: R.159, R.160 Chain D: T.39, E.40 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: T.39, E.40 Chain D: R.159, R.160 Ligand excluded by PLIP

14 x V6V: 5-bromo-3-methyl-1H-indole-2-carboxylic acid(Non-covalent)

V6V.7: 12 residues within 4Å: Chain A: G.37, R.38, T.39, Q.73 Chain C: I.72, Q.73, R.160, H.161, P.162, E.163, T.164, G.165 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.72 Hydrogen bonds: C:Q.73, C:E.163, A:Q.73 Water bridges: C:I.72, C:Q.73 Halogen bonds: A:T.39 V6V.8: 4 residues within 4Å: Chain A: R.58, V.59, L.60, P.61 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.58, A:L.60 V6V.9: 11 residues within 4Å: Chain A: I.72, Q.73, R.160, H.161, P.162, E.163, T.164, G.165 Chain C: G.37, R.38, T.39 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.72 Hydrogen bonds: A:Q.73, A:E.163, A:E.163 Water bridges: A:I.72, A:Q.73 Halogen bonds: C:T.39 V6V.10: 9 residues within 4Å: Chain A: A.2, M.3, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: ACT.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.79, A:K.91, A:K.91, A:K.91, A:N.93 Hydrogen bonds: A:N.93 Water bridges: A:M.3, A:M.3 pi-Cation interactions: A:R.79, A:R.79 V6V.11: 5 residues within 4Å: Chain A: R.29, L.30, Q.81, A.82, M.83 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.29 V6V.18: 12 residues within 4Å: Chain B: G.37, R.38, T.39, Q.73 Chain D: I.72, Q.73, R.160, H.161, P.162, E.163, T.164, G.165 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:I.72 Hydrogen bonds: D:Q.73, D:E.163, B:Q.73 Water bridges: D:I.72, D:Q.73 Halogen bonds: B:T.39 V6V.19: 4 residues within 4Å: Chain B: R.58, V.59, L.60, P.61 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.58, B:L.60 V6V.20: 11 residues within 4Å: Chain B: I.72, Q.73, R.160, H.161, P.162, E.163, T.164, G.165 Chain D: G.37, R.38, T.39 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain B Halogen bonds: D:T.39 Hydrophobic interactions: B:I.72 Hydrogen bonds: B:Q.73, B:E.163, B:E.163 Water bridges: B:I.72, B:Q.73 V6V.21: 9 residues within 4Å: Chain B: A.2, M.3, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: ACT.14 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:R.79, B:K.91, B:K.91, B:K.91, B:N.93 Hydrogen bonds: B:N.93 Water bridges: B:M.3, B:M.3 pi-Cation interactions: B:R.79, B:R.79 V6V.22: 5 residues within 4Å: Chain B: R.29, L.30, Q.81, A.82, M.83 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.29 V6V.28: 4 residues within 4Å: Chain C: R.58, V.59, L.60, P.61 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:R.58, C:L.60 V6V.29: 5 residues within 4Å: Chain C: R.29, L.30, E.31, Q.81, A.82 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:R.29 V6V.35: 4 residues within 4Å: Chain D: R.58, V.59, L.60, P.61 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:R.58, D:L.60 V6V.36: 5 residues within 4Å: Chain D: R.29, L.30, E.31, Q.81, A.82 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:R.29

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
B

B
B

C
A

D
A

Advanced glycosylation end product-specific receptor

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