- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- monomer
- Ligands
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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
- 2 x ZN: ZINC ION(Non-covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 1 x K: POTASSIUM ION(Non-covalent)
- 2 x SCN: THIOCYANATE ION(Non-functional Binders)
- 17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.11: 7 residues within 4Å:- Chain A: P.509, R.788, E.791, D.797, Y.806, L.810, K.813
Ligand excluded by PLIPEDO.12: 9 residues within 4Å:- Chain A: I.116, C.159, G.160, Y.455, G.456, F.459, K.460, Y.461, R.500
Ligand excluded by PLIPEDO.13: 7 residues within 4Å:- Chain A: G.639, F.640, P.644, Y.645, W.673, T.674, Q.677
Ligand excluded by PLIPEDO.14: 5 residues within 4Å:- Chain A: Y.566, F.586, F.699, R.707, D.708
Ligand excluded by PLIPEDO.15: 3 residues within 4Å:- Chain A: R.157, H.162, K.464
Ligand excluded by PLIPEDO.16: 7 residues within 4Å:- Chain A: Y.666, Y.701, Q.715, V.724, P.725, T.726, H.758
Ligand excluded by PLIPEDO.17: 3 residues within 4Å:- Chain A: K.386, L.411, E.413
Ligand excluded by PLIPEDO.18: 4 residues within 4Å:- Chain A: P.485, A.486, P.487, N.488
Ligand excluded by PLIPEDO.19: 6 residues within 4Å:- Chain A: I.585, F.586, E.710, Y.716, S.721, P.723
Ligand excluded by PLIPEDO.20: 6 residues within 4Å:- Chain A: L.749, S.750, V.751, L.812, Y.815
- Ligands: EDO.26
Ligand excluded by PLIPEDO.21: 3 residues within 4Å:- Chain A: L.565, R.707, G.795
Ligand excluded by PLIPEDO.22: 3 residues within 4Å:- Chain A: N.339, K.379, K.380
Ligand excluded by PLIPEDO.23: 6 residues within 4Å:- Chain A: F.669, P.757, R.759, D.761, N.762, L.779
Ligand excluded by PLIPEDO.24: 6 residues within 4Å:- Chain A: K.386, E.764, S.765, E.778, L.779, M.782
Ligand excluded by PLIPEDO.25: 6 residues within 4Å:- Chain A: G.191, N.402, R.403, R.404
- Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN.2
Ligand excluded by PLIPEDO.26: 7 residues within 4Å:- Chain A: R.688, S.750, V.751, S.752, Y.815, H.817
- Ligands: EDO.20
Ligand excluded by PLIPEDO.27: 7 residues within 4Å:- Chain A: Q.391, H.392, T.726, H.727, P.757, H.758, R.759
Ligand excluded by PLIP- 1 x DWX: [3-({4-[(5Z)-5-(3,4-dichlorobenzylidene)-4-oxo-4,5-dihydro-1,3-thiazol-2-yl]piperazin-1-yl}methyl)phenyl]boronic acid(Non-covalent)
DWX.28: 19 residues within 4Å:- Chain A: S.134, D.136, K.173, T.174, F.175, L.178, A.182, N.195, L.208, F.238, F.239, W.240, R.249, Y.271, D.276, H.324, H.439
- Ligands: ZN.4, ZN.5
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:F.175, A:L.208, A:F.238, A:Y.271
- Hydrogen bonds: A:T.174, A:N.195, A:W.240, A:R.249, A:D.276
- pi-Stacking: A:F.239, A:Y.271
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kawaguchi, M. et al., Screening and X-ray Crystal Structure-based Optimization of Autotaxin (ENPP2) Inhibitors, Using a Newly Developed Fluorescence Probe. Acs Chem.Biol. (2013)
- Release Date
- 2013-07-31
- Peptides
- Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- monomer
- Ligands
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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
- 2 x ZN: ZINC ION(Non-covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 1 x K: POTASSIUM ION(Non-covalent)
- 2 x SCN: THIOCYANATE ION(Non-functional Binders)
- 17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x DWX: [3-({4-[(5Z)-5-(3,4-dichlorobenzylidene)-4-oxo-4,5-dihydro-1,3-thiazol-2-yl]piperazin-1-yl}methyl)phenyl]boronic acid(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kawaguchi, M. et al., Screening and X-ray Crystal Structure-based Optimization of Autotaxin (ENPP2) Inhibitors, Using a Newly Developed Fluorescence Probe. Acs Chem.Biol. (2013)
- Release Date
- 2013-07-31
- Peptides
- Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A