SMTL ID : 4lqg.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a phosphoramidate inhibitor CTT1056

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

2 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.35, Q.38, Q.54, S.57, Q.58 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.54 Hydrogen bonds: A:S.57 NAG-NAG.13: 5 residues within 4Å: Chain B: N.35, Q.38, Q.54, S.57, Q.58 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.54 Hydrogen bonds: B:S.57

4 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 4 residues within 4Å: Chain A: N.80, T.82, H.83, T.308 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.3: 5 residues within 4Å: Chain A: Y.86, E.96, I.97, N.99, L.102 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.86, A:L.102 NAG-NAG-FUC.14: 4 residues within 4Å: Chain B: N.80, T.82, H.83, T.308 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 5 residues within 4Å: Chain B: Y.86, E.96, I.97, N.99, L.102 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.86, B:L.102

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

NAG-NAG-BMA.4: 5 residues within 4Å: Chain A: S.431, L.432, N.435, P.553, Q.610 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.611, A:D.611 Water bridges: A:Q.610 NAG-NAG-BMA.16: 5 residues within 4Å: Chain B: S.431, L.432, N.435, P.553, Q.610 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.611, B:D.611 Water bridges: B:Q.610

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.5: 10 residues within 4Å: Chain A: S.590, S.593, A.594, N.597, Q.699 Chain B: L.69, H.71, E.235, Y.236, R.313 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.235, B:R.313, B:R.313, B:L.69 Water bridges: B:H.71, B:Q.56, B:L.69, B:H.71 NAG-NAG-BMA-MAN-MAN.17: 10 residues within 4Å: Chain A: L.69, H.71, E.235, Y.236, R.313 Chain B: S.590, S.593, A.594, N.597, Q.699 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.235, A:R.313, A:R.313, A:L.69 Water bridges: A:H.71, A:Q.56, A:L.69, A:H.71

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: D.346, E.384, Y.511, H.512 Ligands: ZN.7, CTW.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.346, A:E.384, A:E.384, A:H.512 ZN.7: 7 residues within 4Å: Chain A: H.336, D.346, E.383, E.384, D.412 Ligands: ZN.6, CTW.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.336, A:D.346, A:D.412, A:D.412 ZN.18: 6 residues within 4Å: Chain B: D.346, E.384, Y.511, H.512 Ligands: ZN.19, CTW.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.346, B:E.384, B:E.384, B:H.512 ZN.19: 7 residues within 4Å: Chain B: H.336, D.346, E.383, E.384, D.412 Ligands: ZN.18, CTW.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.336, B:D.346, B:D.412, B:D.412

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: T.228, Y.231, E.392, E.395 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.228, A:Y.231, A:E.392, A:E.392, A:E.395 CA.20: 4 residues within 4Å: Chain B: T.228, Y.231, E.392, E.395 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.228, B:Y.231, B:E.392, B:E.392, B:E.395

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

CL.9: 5 residues within 4Å: Chain A: N.410, D.412, R.493, R.495, R.539 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain B: N.410, D.412, R.493, R.495, R.539 Ligand excluded by PLIP

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

NAG.10: 2 residues within 4Å: Chain A: N.154, S.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.156 NAG.11: 4 residues within 4Å: Chain A: W.205, N.418, F.524, Y.525 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.205, A:Y.525 Hydrogen bonds: A:W.205, A:F.524 Water bridges: A:N.418 NAG.22: 2 residues within 4Å: Chain B: N.154, S.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.156 NAG.23: 4 residues within 4Å: Chain B: W.205, N.418, F.524, Y.525 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.205, B:Y.525 Hydrogen bonds: B:W.205, B:F.524 Water bridges: B:N.418

2 x CTW: N-(4-fluorobenzoyl)-L-gamma-glutamyl-5-{[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]oxy}-L-norvaline(Non-covalent)

CTW.12: 24 residues within 4Å: Chain A: R.169, N.216, H.336, D.346, E.383, E.384, G.386, L.387, D.412, R.422, S.472, G.477, N.478, R.493, R.495, W.500, Y.511, H.512, N.657, K.658, Y.659, A.660 Ligands: ZN.6, ZN.7 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.387, A:Y.659, A:Y.659 Hydrogen bonds: A:N.216, A:R.422, A:R.422, A:G.477, A:N.478, A:Y.511, A:N.657 Water bridges: A:R.493, A:R.493, A:R.495, A:K.658, A:G.661 Salt bridges: A:R.169, A:R.422, A:R.493, A:R.495, A:H.512, A:K.658 pi-Cation interactions: A:R.422 CTW.24: 24 residues within 4Å: Chain B: R.169, N.216, H.336, D.346, E.383, E.384, G.386, L.387, D.412, R.422, S.472, G.477, N.478, R.493, R.495, W.500, Y.511, H.512, N.657, K.658, Y.659, A.660 Ligands: ZN.18, ZN.19 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.387, B:Y.659, B:Y.659 Hydrogen bonds: B:N.216, B:R.422, B:R.422, B:G.477, B:N.478, B:Y.511, B:N.657 Water bridges: B:R.493, B:R.493, B:R.495, B:K.658, B:G.661 Salt bridges: B:R.169, B:R.422, B:R.493, B:R.495, B:H.512, B:K.658 pi-Cation interactions: B:R.422

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dannoon, S. et al., Structure-Activity Relationship of (18)F-Labeled Phosphoramidate Peptidomimetic Prostate-Specific Membrane Antigen (PSMA)-Targeted Inhibitor Analogues for PET Imaging of Prostate Cancer. J.Med.Chem. (2016)

Release Date

2014-12-31

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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