SMTL ID : 4ngp.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 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: Y.116, E.126, I.127, N.129 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.65, Q.68, Q.84, S.87, Q.88 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: W.235, N.448, F.554, Y.555 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: Y.116, E.126, I.127, N.129 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: N.65, Q.68, Q.84, S.87, Q.88 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: W.235, N.448, F.554, Y.555 No protein-ligand interaction detected (PLIP)

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.3: 10 residues within 4Å: Chain A: S.620, S.623, A.624, N.627, Q.729 Chain B: L.99, H.101, E.265, Y.266, R.343 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.343, B:R.343, B:L.99 Water bridges: B:H.101, B:R.343, B:L.99 NAG-NAG-BMA-MAN-MAN.15: 10 residues within 4Å: Chain A: L.99, H.101, E.265, Y.266, R.343 Chain B: S.620, S.623, A.624, N.627, Q.729 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.343, A:R.343, A:L.99 Water bridges: A:H.101, A:R.343, A:L.99

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.461, L.462, N.465, P.583, Q.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.640, A:Q.640 Water bridges: A:R.587 NAG-NAG-BMA.16: 5 residues within 4Å: Chain B: S.461, L.462, N.465, P.583, Q.640 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.640, B:Q.640 Water bridges: B:R.587

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

NAG.6: 2 residues within 4Å: Chain A: N.184, S.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.184, A:S.186 NAG.7: 4 residues within 4Å: Chain A: N.110, T.112, H.113, T.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.110 Water bridges: A:Q.156 NAG.18: 2 residues within 4Å: Chain B: N.184, S.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.184, B:S.186 NAG.19: 4 residues within 4Å: Chain B: N.110, T.112, H.113, T.338 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.110 Water bridges: B:Q.156

2 x J31: N-{[(1S)-1-carboxy-5-{[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)benzoyl]amino}pentyl]carbamoyl}-L-glutamic acid(Non-covalent)

J31.8: 24 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, W.530, N.533, F.535, Y.541, H.542, N.687, K.688, Y.689, A.690 Ligands: ZN.10 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:W.530, A:F.535, A:Y.689 Hydrogen bonds: A:N.246, A:N.246, A:G.507, A:G.507, A:G.507, A:N.508, A:Y.541, A:N.687, A:Y.689 Water bridges: A:N.246, A:E.446, A:R.452, A:R.452, A:R.523, A:K.688 Salt bridges: A:R.199, A:R.523, A:R.525, A:H.542, A:K.688 J31.20: 24 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, W.530, N.533, F.535, Y.541, H.542, N.687, K.688, Y.689, A.690 Ligands: ZN.22 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:W.530, B:F.535, B:Y.689 Hydrogen bonds: B:N.246, B:N.246, B:G.507, B:G.507, B:G.507, B:N.508, B:Y.541, B:N.687, B:Y.689 Water bridges: B:N.246, B:E.446, B:R.452, B:R.452, B:R.523, B:K.688 Salt bridges: B:R.199, B:R.523, B:R.525, B:H.542, B:K.688

4 x ZN: ZINC ION(Non-covalent)

ZN.9: 6 residues within 4Å: Chain A: H.366, D.376, E.413, E.414, D.442 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.366, A:D.376, A:D.442, A:D.442, H2O.18 ZN.10: 5 residues within 4Å: Chain A: D.376, E.414, H.542 Ligands: J31.8, ZN.9 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.18 ZN.21: 6 residues within 4Å: Chain B: H.366, D.376, E.413, E.414, D.442 Ligands: ZN.22 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.366, B:D.376, B:D.442, B:D.442, H2O.42 ZN.22: 5 residues within 4Å: Chain B: D.376, E.414, H.542 Ligands: J31.20, ZN.21 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.42

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

CL.11: 4 residues within 4Å: Chain A: N.440, D.442, R.523, R.525 Ligand excluded by PLIP CL.23: 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.12: 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.24: 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

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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