SMTL ID : 3wav.1

Crystal Structure of Autotaxin in Complex with Compound 10

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.18, S.20 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Y.340, L.341, T.342, N.375 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.2: 15 residues within 4Å: Chain A: L.185, E.188, S.189, H.190, G.220, H.398, N.401, N.402, P.487, N.488, N.489, N.704, L.706, H.792 Ligands: EDO.25 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.188 Water bridges: A:S.189, A:N.401, A:N.401, A:N.401

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: D.136, T.174, D.276, D.323, H.324 Ligands: SO4.29 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.136, A:D.136, A:T.174, A:D.323, A:H.324 ZN.5: 4 residues within 4Å: Chain A: D.276, H.280, H.439 Ligands: SO4.29 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.700, N.702, N.704, L.706, D.708 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.700, A:L.706, A:D.708, H2O.2

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

NA.7: 4 residues within 4Å: Chain A: N.762, D.763, S.765, S.768 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.768 Water bridges: A:S.768

1 x K: POTASSIUM ION(Non-covalent)

K.8: 3 residues within 4Å: Chain A: Y.630, D.633, M.636 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.630, A:D.633, A:M.636, H2O.17

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.9: 5 residues within 4Å: Chain A: S.196, M.197, Y.198, V.350, R.358 No protein-ligand interaction detected (PLIP) SCN.10: 5 residues within 4Å: Chain A: K.173, G.194, N.195, L.354, R.356 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.195

18 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 PLIP EDO.12: 8 residues within 4Å: Chain A: I.116, C.159, G.160, Y.455, G.456, F.459, K.460, Y.461 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: G.639, F.640, P.643, P.644, Y.645, W.673, Q.677 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: Y.566, F.586, F.699, R.707, D.708 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: R.157, H.162, K.464 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: Y.666, Y.701, Q.715, V.724, P.725, T.726, H.758 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: K.386, L.411, V.412, E.413 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: I.357, R.358, Y.367, E.406, D.407, L.408 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: I.585, F.586, E.710, Y.716, S.721, P.723 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: L.736, S.750, V.751, L.812, Y.815 Ligands: EDO.26 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: L.565, R.707, G.795 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: N.339, K.379, K.380 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: F.669, P.757, H.758, R.759, D.761, N.762, L.779 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: K.386, E.764, S.765, E.778, L.779, M.782 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: G.191, N.402, R.403, R.404 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN.2 Ligand excluded by PLIP EDO.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 PLIP EDO.27: 6 residues within 4Å: Chain A: H.392, T.726, H.727, P.757, H.758, R.759 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: E.115, K.460, Y.461, R.500 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.29: 10 residues within 4Å: Chain A: D.136, K.173, T.174, N.195, L.208, D.276, H.280, H.439 Ligands: ZN.4, ZN.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.174, A:T.174, A:N.195 Water bridges: A:K.173, A:K.173 Salt bridges: A:H.280, A:H.439

1 x DWV: (5Z)-5-(3,4-dichlorobenzylidene)-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4(5H)-one(Non-covalent)

DWV.30: 12 residues within 4Å: Chain A: S.134, T.174, F.175, L.178, A.182, L.208, W.225, F.238, F.239, W.240, A.269, Y.271 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.239, A:F.239, A:A.269, A:Y.271 Hydrogen bonds: A:W.240 Water bridges: A:R.249 pi-Stacking: A:F.238, 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

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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