SMTL ID : 4ngt.1

Crystal Structure of Glutamate Carboxypeptidase II in a complex with urea-based inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 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: 4 residues within 4Å: Chain A: S.461, L.462, N.465, P.583 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: S.461, L.462, N.465, P.583 No protein-ligand interaction detected (PLIP)

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.2: 8 residues within 4Å: Chain A: S.620, S.623, A.624, N.627, Q.729 Chain B: H.101, E.265, R.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.265, B:R.343, B:R.343 NAG-NAG-BMA.14: 8 residues within 4Å: Chain A: H.101, E.265, R.343 Chain B: S.620, S.623, A.624, N.627, Q.729 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.265, A:R.343, A:R.343

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

NAG.3: 3 residues within 4Å: Chain A: N.65, Q.68, Q.84 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.68 Hydrogen bonds: A:N.65 Water bridges: A:N.65, A:Q.84 NAG.4: 4 residues within 4Å: Chain A: N.110, T.112, H.113, T.338 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110 NAG.5: 4 residues within 4Å: Chain A: Y.116, E.126, I.127, N.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.126, A:N.129 NAG.6: 4 residues within 4Å: Chain A: W.235, N.448, F.554, Y.555 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.235, A:Y.555 Hydrogen bonds: A:W.235, A:F.554 Water bridges: A:N.448 NAG.15: 3 residues within 4Å: Chain B: N.65, Q.68, Q.84 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.68 Hydrogen bonds: B:N.65 Water bridges: B:N.65, B:Q.84 NAG.16: 4 residues within 4Å: Chain B: N.110, T.112, H.113, T.338 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.110 NAG.17: 4 residues within 4Å: Chain B: Y.116, E.126, I.127, N.129 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.126, B:N.129 NAG.18: 4 residues within 4Å: Chain B: W.235, N.448, F.554, Y.555 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.235, B:Y.555 Hydrogen bonds: B:W.235, B:F.554 Water bridges: B:N.448

4 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: H.366, D.376, E.413, E.414, D.442 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.366, A:D.376, A:D.376, A:D.442, H2O.2 ZN.8: 5 residues within 4Å: Chain A: D.376, E.414, H.542 Ligands: ZN.7, J42.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.376, A:E.414, A:E.414, A:H.542, H2O.2 ZN.19: 6 residues within 4Å: Chain B: H.366, D.376, E.413, E.414, D.442 Ligands: ZN.20 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.366, B:D.376, B:D.376, B:D.442, H2O.13 ZN.20: 5 residues within 4Å: Chain B: D.376, E.414, H.542 Ligands: ZN.19, J42.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.376, B:E.414, B:E.414, B:H.542, H2O.13

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

CL.9: 4 residues within 4Å: Chain A: N.440, D.442, R.523, R.525 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: N.440, D.442, R.523, R.525 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: T.258, Y.261, E.422, E.425 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.258, A:Y.261, A:E.422, A:E.422, A:E.425 CA.22: 4 residues within 4Å: Chain B: T.258, Y.261, E.422, E.425 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.258, B:Y.261, B:E.422, B:E.422, B:E.425

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

NA.11: 4 residues within 4Å: Chain A: R.452, V.453, D.454, S.502 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.453, A:D.454, A:S.502 NA.23: 4 residues within 4Å: Chain B: R.452, V.453, D.454, S.502 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.453, B:V.453, B:S.502

2 x J42: N-{[(1S)-5-({[4-bromo-2-({4,44-dioxo-48-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-7,10,13,16,19,22,25,28,31,34,37,40-dodecaoxa-3,43-diazaoctatetracont-1-yl}oxy)phenyl]carbamoyl}amino)-1-carboxypentyl]carbamoyl}-L-glutamic acid(Non-covalent)

J42.12: 23 residues within 4Å: Chain A: F.198, R.199, N.246, D.376, E.413, E.414, G.416, L.417, E.446, R.452, G.507, N.508, R.523, R.525, T.527, K.528, W.530, Y.541, H.542, K.688, Y.689, A.690 Ligands: ZN.8 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.689, A:Y.689, A:A.690 Hydrogen bonds: A:N.246, A:G.507, A:G.507, A:N.508, A:Y.541, A:Y.689 Water bridges: A:N.246, A:D.376, A:D.376, A:E.414, A:R.452, A:R.452, A:R.523, A:K.688, A:G.691 Salt bridges: A:R.199, A:R.523, A:R.525, A:H.542, A:K.688 Halogen bonds: A:K.528 J42.24: 23 residues within 4Å: Chain B: F.198, R.199, N.246, D.376, E.413, E.414, G.416, L.417, E.446, R.452, G.507, N.508, R.523, R.525, T.527, K.528, W.530, Y.541, H.542, K.688, Y.689, A.690 Ligands: ZN.20 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.689, B:Y.689, B:A.690 Hydrogen bonds: B:N.246, B:G.507, B:G.507, B:N.508, B:Y.541, B:Y.689 Water bridges: B:N.246, B:D.376, B:E.414, B:R.452, B:R.452, B:R.523, B:K.688, B:G.691 Salt bridges: B:R.199, B:R.523, B:R.525, B:H.542, B:K.688 Halogen bonds: B:K.528

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tykvart, J. et al., Rational design of urea-based glutamate carboxypeptidase II (GCPII) inhibitors as versatile tools for specific drug targeting and delivery. Bioorg.Med.Chem. (2014)

Release Date

2014-06-18

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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