SMTL ID : 7ld9.1

Structure of human GGT1 in complex with ABBA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

hetero-1-1-mer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 6 residues within 4Å: Chain A: N.68, T.70, T.71, R.120, H.121, R.123 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.121 Hydrogen bonds: A:N.68, A:R.123, A:R.123 NAG.2: 5 residues within 4Å: Chain A: F.88, T.90, M.91, N.93, Q.97 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.97 Hydrogen bonds: A:M.91, A:N.93, A:Q.97 Water bridges: A:T.90, A:M.91 NAG.3: 4 residues within 4Å: Chain A: E.313, N.317, F.323, Q.326 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.313 Hydrogen bonds: A:N.317, A:Q.326, A:Q.326 NAG.4: 4 residues within 4Å: Chain A: H.236, N.239, V.246, Y.248 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.246 Water bridges: A:N.239, A:N.239, A:N.239 NAG.5: 4 residues within 4Å: Chain A: N.203, G.204, T.207, N.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.203, A:N.227 NAG.9: 6 residues within 4Å: Chain A: T.336, H.337, P.338, I.339 Chain B: N.131, H.151 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.151, A:I.339 Water bridges: B:N.131, B:H.153 Hydrophobic interactions: A:I.339

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

CL.6: 6 residues within 4Å: Chain A: V.167, L.183, P.184, Q.185, L.186 Chain B: R.29 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain A: D.19 Chain B: A.2, H.3, A.92, V.163, Q.165, K.182 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain A: D.7, N.8, H.9 Chain B: K.116, A.176, A.177 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:K.116, B:A.176 Hydrogen bonds: A:H.9

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 9 residues within 4Å: Chain A: C.165, E.166, V.167, C.169, R.170, D.171, R.172, T.182, P.184 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.165, A:R.172, A:T.182 Water bridges: A:D.171 Salt bridges: A:E.166, A:E.166 EPE.13: 7 residues within 4Å: Chain B: L.22, Y.23, G.93, Q.96, T.159, F.160, A.162 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.23, B:A.162 Water bridges: B:Q.96, B:T.159, A:K.154, A:K.154 EPE.14: 10 residues within 4Å: Chain A: Q.99 Chain B: N.21, D.42, D.43, F.44, S.45, N.51, P.57, S.58, N.61 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.21, B:N.21, B:D.43, B:S.45, B:S.58, B:S.58, B:N.61 Water bridges: B:N.51, A:R.300, A:R.300 Salt bridges: B:D.42, B:D.43

1 x XUJ: (2R)-2-amino-4-boronobutanoic acid(Covalent)

XUJ.11: 12 residues within 4Å: Chain A: R.80 Chain B: T.1, T.19, N.21, E.40, D.43, S.71, S.72, M.73, G.93, G.94 Ligands: XU7.12 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.1, B:T.19, B:E.40, B:D.43, B:S.72, B:S.72, B:M.73, B:G.93, B:G.94 Water bridges: B:N.21 Salt bridges: A:R.80

1 x XU7: (2S)-2-amino-4-boronobutanoic acid(Covalent)

XU7.12: 12 residues within 4Å: Chain A: R.80 Chain B: T.1, T.19, N.21, E.40, D.43, S.71, S.72, M.73, G.93, G.94 Ligands: XUJ.11 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.1, B:T.1, B:T.1, B:T.19, B:N.21, B:E.40, B:S.72, B:S.72, B:M.73, B:G.93, B:G.94 Salt bridges: A:R.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, L. et al., Design and evaluation of novel analogs of 2-amino-4-boronobutanoic acid (ABBA) as inhibitors of human gamma-glutamyl transpeptidase. Bioorg.Med.Chem. (2022)

Release Date

2022-02-23

Peptides

Glutathione hydrolase 1 heavy chain: A
Glutathione hydrolase 1 light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutathione hydrolase 1 heavy chain

Glutathione hydrolase 1 light chain

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