SMTL ID : 3iww.1

Crystal structure of human glutamate carboxypeptidase II (GCPII) in a complex with DBIBzL, a urea-based inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

6 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: 4 residues within 4Å: Chain A: N.35, Q.54, S.57, Q.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.57 NAG-NAG.2: 4 residues within 4Å: Chain A: Y.86, E.96, I.97, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.435, P.553 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.35, Q.54, S.57, Q.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.57 NAG-NAG.14: 4 residues within 4Å: Chain B: Y.86, E.96, I.97, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.435, P.553 No protein-ligand interaction detected (PLIP)

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.4: 9 residues within 4Å: Chain A: S.590, S.593, A.594, N.597, Q.699 Chain B: H.71, E.235, Y.236, R.313 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.235, B:E.235 Hydrogen bonds: B:E.235, B:R.313, B:R.313 NAG-NAG-BMA-MAN.16: 9 residues within 4Å: Chain A: H.71, E.235, Y.236, R.313 Chain B: S.590, S.593, A.594, N.597, Q.699 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.235, A:E.235 Hydrogen bonds: A:E.235, A:R.313, A:R.313

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: D.346, E.383, E.384, H.512 Ligands: ZN.6, YZE.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.346, A:E.384, A:E.384, A:H.512, H2O.2 ZN.6: 6 residues within 4Å: Chain A: H.336, D.346, E.383, E.384, D.412 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.336, A:D.346, A:D.412, A:D.412, H2O.2 ZN.17: 6 residues within 4Å: Chain B: D.346, E.383, E.384, H.512 Ligands: ZN.18, YZE.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.346, B:E.384, B:E.384, B:H.512, H2O.11 ZN.18: 6 residues within 4Å: Chain B: H.336, D.346, E.383, E.384, D.412 Ligands: ZN.17 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.336, B:D.346, B:D.412, B:D.412, H2O.11

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: T.228, Y.231, E.392, E.395 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.228, A:E.392, A:E.392, A:E.395, H2O.2 CA.19: 4 residues within 4Å: Chain B: T.228, Y.231, E.392, E.395 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.228, B:E.392, B:E.392, B:E.395, H2O.11

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

CL.8: 5 residues within 4Å: Chain A: N.410, D.412, R.493, R.495, R.539 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: N.410, D.412, R.493, R.495, R.539 Ligand excluded by PLIP

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

NAG.9: 3 residues within 4Å: Chain A: N.80, H.83, T.308 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.308 Hydrogen bonds: A:T.82 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.21: 3 residues within 4Å: Chain B: N.80, H.83, T.308 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.308 Hydrogen bonds: B:T.82 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 YZE: N~2~-{[(1S)-1-carboxybut-3-en-1-yl]carbamoyl}-N~6~-[(4-iodophenyl)carbonyl]-L-lysine(Non-covalent)

YZE.12: 23 residues within 4Å: Chain A: R.169, N.216, L.220, D.346, E.383, E.384, G.386, L.387, D.412, E.416, R.422, D.424, G.477, N.478, R.493, R.495, K.504, F.505, G.507, Y.511, H.512, Y.659 Ligands: ZN.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.220, A:L.387, A:Y.511, A:Y.659 Hydrogen bonds: A:G.477, A:G.477, A:N.478, A:Y.511 Water bridges: A:N.216, A:E.416, A:G.507 Salt bridges: A:R.169, A:R.493, A:R.495, A:H.512 pi-Cation interactions: A:R.422, A:R.493 Halogen bonds: A:R.422 YZE.24: 23 residues within 4Å: Chain B: R.169, N.216, L.220, D.346, E.383, E.384, G.386, L.387, D.412, E.416, R.422, D.424, G.477, N.478, R.493, R.495, K.504, F.505, G.507, Y.511, H.512, Y.659 Ligands: ZN.17 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.220, B:L.387, B:Y.511, B:Y.659 Hydrogen bonds: B:G.477, B:G.477, B:N.478, B:Y.511 Water bridges: B:N.216, B:E.416, B:G.507 Salt bridges: B:R.169, B:R.493, B:R.495, B:H.512 pi-Cation interactions: B:R.422, B:R.493 Halogen bonds: B:R.422

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Bioisosterism of urea-based GCPII inhibitors: Synthesis and structure-activity relationship studies. Bioorg.Med.Chem.Lett. (2010)

Release Date

2009-11-24

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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