SMTL ID : 7mfh.1

Crystal structure of BIO-32546 bound mouse Autotaxin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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.1: 13 residues within 4Å: Chain A: L.186, E.189, S.190, G.221, H.399, N.402, N.403, P.488, N.489, N.490, G.706, L.707, H.793 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.190, A:N.402, A:N.402

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: L.342, T.343, N.344, N.376 No protein-ligand interaction detected (PLIP)

1 x ZF7: (1R,3S,5S)-8-{(1S)-1-[8-(trifluoromethyl)-7-{[(1s,4R)-4-(trifluoromethyl)cyclohexyl]oxy}naphthalen-2-yl]ethyl}-8-azabicyclo[3.2.1]octane-3-carboxylic acid(Non-covalent)

ZF7.3: 19 residues within 4Å: Chain A: L.44, Y.48, I.133, S.135, F.176, L.179, Y.180, A.183, K.214, F.215, H.217, W.220, L.225, W.226, F.239, F.240, Y.272, M.478 Ligands: EDO.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.176, A:L.179, A:L.179, A:W.220, A:W.220, A:F.240, A:F.240, A:F.240, A:Y.272 Salt bridges: A:H.217 pi-Stacking: A:F.176, A:Y.272

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 1 residues within 4Å: Chain A: S.244 Ligand excluded by PLIP

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 3 residues within 4Å: Chain A: H.217, W.226 Ligands: ZF7.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.217 EDO.7: 7 residues within 4Å: Chain A: Y.567, T.569, F.587, R.708, I.710, E.711 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.711, A:E.711 EDO.8: 6 residues within 4Å: Chain A: Y.567, F.587, F.700, R.708, D.709 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.709 EDO.9: 7 residues within 4Å: Chain A: G.640, F.641, K.671, W.674, T.675, Q.678, R.679 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.641, A:F.641, A:T.675, A:Q.678, A:R.679 EDO.10: 4 residues within 4Å: Chain A: S.638, P.668, K.671 Ligands: EDO.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.638, A:K.671 EDO.11: 5 residues within 4Å: Chain A: N.763, D.764, S.766, S.769 Ligands: PEG.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.763, A:D.764, A:S.766, A:S.769 EDO.13: 4 residues within 4Å: Chain A: P.507, S.806, Y.807, S.808 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.806, A:Y.807, A:S.808 Water bridges: A:S.808 EDO.16: 7 residues within 4Å: Chain A: Y.187, R.397, H.399, E.470, R.787, D.790, L.817 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.790 Water bridges: A:R.397, A:N.444 EDO.17: 6 residues within 4Å: Chain A: G.125, F.126, V.127, R.265, P.266, S.267 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.127, A:R.265 EDO.18: 7 residues within 4Å: Chain A: C.89, L.90, G.93, D.94, C.95, Q.310, L.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.93, A:C.95, A:Q.310 EDO.19: 3 residues within 4Å: Chain A: I.227, T.230, K.231 No protein-ligand interaction detected (PLIP) EDO.20: 3 residues within 4Å: Chain A: P.165, P.467, P.468 No protein-ligand interaction detected (PLIP) EDO.25: 8 residues within 4Å: Chain A: A.669, F.670, V.673, P.758, R.760, D.762, N.763, L.780 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.760, A:R.760 EDO.26: 4 residues within 4Å: Chain A: Y.631, K.632, S.638 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.631, A:S.638

7 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: D.701, N.703, N.705, L.707, D.709 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.701, A:L.707, A:D.709, H2O.1 ZN.14: 4 residues within 4Å: Chain A: T.175, D.277, H.281, H.440 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.277, A:D.277, A:H.281, A:H.440, H2O.6 ZN.15: 3 residues within 4Å: Chain A: P.749, L.750, E.809 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.809 ZN.21: 4 residues within 4Å: Chain A: H.247, F.271, S.273, T.300 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.247, A:S.273 ZN.22: 2 residues within 4Å: Chain A: W.241, R.250 No protein-ligand interaction detected (PLIP) ZN.23: 3 residues within 4Å: Chain A: M.198, Y.199, R.359 No protein-ligand interaction detected (PLIP) ZN.24: 6 residues within 4Å: Chain A: K.174, G.195, N.196, S.197, L.355, R.357 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 7 residues within 4Å: Chain A: P.668, A.669, R.672, D.762, N.763, D.764 Ligands: EDO.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.672, A:N.763, A:N.763, A:D.764

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, B. et al., Discovery of Potent Selective Nonzinc Binding Autotaxin Inhibitor BIO-32546. Acs Med.Chem.Lett. (2021)

Release Date

2022-04-13

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2