SMTL ID : 6rbc.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor KB1157

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.33, Q.36, Q.52, S.55, Q.56 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: S.429, L.430, N.433, P.551, Q.608 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.608 NAG-NAG.13: 5 residues within 4Å: Chain B: N.33, Q.36, Q.52, S.55, Q.56 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: S.429, L.430, N.433, P.551, Q.608 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.608

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.3: 9 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, Q.697 Chain B: H.69, E.233, Y.234, R.311 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.233, B:R.311, B:R.311 Water bridges: B:H.69 NAG-NAG-BMA-MAN.15: 9 residues within 4Å: Chain A: H.69, E.233, Y.234, R.311 Chain B: S.588, S.591, A.592, N.595, Q.697 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.233, A:R.311, A:R.311 Water bridges: A:H.69

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

NAG.4: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.306 Hydrogen bonds: A:T.80, A:H.81 NAG.5: 4 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.84, A:E.94, A:E.94, A:N.97 NAG.6: 2 residues within 4Å: Chain A: N.152, S.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.154 NAG.7: 4 residues within 4Å: Chain A: W.203, N.416, F.522, Y.523 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.203, A:Y.523 Hydrogen bonds: A:W.203, A:F.522 Water bridges: A:N.416, A:N.416 NAG.16: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.306 Hydrogen bonds: B:T.80, B:H.81 NAG.17: 4 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.84, B:E.94, B:E.94, B:N.97 NAG.18: 2 residues within 4Å: Chain B: N.152, S.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.154 NAG.19: 4 residues within 4Å: Chain B: W.203, N.416, F.522, Y.523 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.203, B:Y.523 Hydrogen bonds: B:W.203, B:F.522 Water bridges: B:N.416, B:N.416

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: D.344, E.382, H.510 Ligands: ZN.9, JX5.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.344, A:E.382, A:E.382, A:H.510, H2O.14 ZN.9: 7 residues within 4Å: Chain A: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.8, JX5.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.334, A:D.344, A:D.410, A:D.410, H2O.14 ZN.20: 5 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: ZN.21, JX5.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.344, B:E.382, B:E.382, B:H.510, H2O.37 ZN.21: 7 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.20, JX5.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.334, B:D.344, B:D.410, B:D.410, H2O.37

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: T.226, Y.229, E.390, E.393 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.226, A:Y.229, A:E.390, A:E.390, A:E.393 CA.22: 4 residues within 4Å: Chain B: T.226, Y.229, E.390, E.393 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.226, B:Y.229, B:E.390, B:E.390, B:E.393

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

CL.11: 4 residues within 4Å: Chain A: N.408, D.410, R.491, R.493 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain B: N.408, D.410, R.491, R.493 Ligand excluded by PLIP

2 x JX5: (2~{S})-2-[[(2~{R})-2-[4-[(4-iodophenyl)carbonylamino]butanoylamino]-3-oxidanyl-3-oxidanylidene-propyl]carbamoylamino]pentanedioic acid(Non-covalent)

JX5.12: 26 residues within 4Å: Chain A: F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, D.410, E.414, R.420, D.422, G.475, N.476, R.491, R.493, K.502, F.503, S.504, G.505, Y.509, H.510, K.656, Y.657 Ligands: ZN.8, ZN.9 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.385, A:Y.509 Hydrogen bonds: A:N.214, A:R.420, A:R.420, A:G.475, A:G.475, A:G.475, A:N.476, A:Y.509, A:Y.509 Water bridges: A:N.214, A:R.491, A:R.491, A:K.656 Salt bridges: A:R.167, A:R.491, A:R.493, A:H.510, A:K.656 pi-Cation interactions: A:R.420, A:R.491 JX5.24: 26 residues within 4Å: Chain B: F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, D.410, E.414, R.420, D.422, G.475, N.476, R.491, R.493, K.502, F.503, S.504, G.505, Y.509, H.510, K.656, Y.657 Ligands: ZN.20, ZN.21 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.385, B:Y.509 Hydrogen bonds: B:N.214, B:R.420, B:R.420, B:G.475, B:G.475, B:G.475, B:N.476, B:Y.509, B:Y.509 Water bridges: B:N.214, B:R.491, B:R.491, B:K.656 Salt bridges: B:R.167, B:R.491, B:R.493, B:H.510, B:K.656 pi-Cation interactions: B:R.420, B:R.491

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, K. et al., Novel beta- and gamma-Amino Acid-Derived Inhibitors of Prostate-Specific Membrane Antigen. J.Med.Chem. (2020)

Release Date

2020-05-13

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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