SMTL ID : 4zg7.1

Structural basis for inhibition of human autotaxin by four novel compounds

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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.1: 9 residues within 4Å: Chain A: L.167, S.171, H.380, P.469, N.470, N.471, G.691, L.692, H.778 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.258, H.262, H.421 Ligands: NKN.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.258, A:D.258, A:H.262, A:H.421 ZN.3: 6 residues within 4Å: Chain A: D.118, T.156, D.258, D.305, H.306 Ligands: NKN.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.118, A:D.118, A:T.156, A:D.305, A:H.306

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.686, D.688, D.690, L.692, D.694 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.686, A:D.688, A:D.690, A:L.692, A:D.694, H2O.17

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

NA.5: 3 residues within 4Å: Chain A: Y.616, D.619, M.622 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.619, A:M.622 NA.6: 4 residues within 4Å: Chain A: N.748, E.749, S.751, S.754 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.751, A:S.754 Water bridges: A:S.755

1 x 4O0: 3-({6-chloro-7-fluoro-2-methyl-1-[2-oxo-2-(spiro[cyclopropane-1,3'-indol]-1'(2'H)-yl)ethyl]-1H-indol-3-yl}sulfanyl)-2-fluorobenzoic acid(Non-covalent)

4O0.7: 17 residues within 4Å: Chain A: L.25, S.28, F.157, L.160, Y.161, K.195, F.196, H.198, W.201, P.205, W.207, F.221, W.222, S.223, V.224 Ligands: NKN.8, GOL.9 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.25, A:F.157, A:F.196, A:F.196, A:H.198, A:W.201, A:W.201, A:P.205, A:F.221, A:F.221 Hydrogen bonds: A:V.224 pi-Stacking: A:H.198, A:W.201, A:W.207, A:W.207

1 x NKN: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate(Non-covalent)

NKN.8: 20 residues within 4Å: Chain A: I.114, D.118, K.155, T.156, F.157, L.160, A.164, N.177, L.190, L.206, F.221, Y.253, D.258, H.262, H.306, H.421, M.459 Ligands: ZN.2, ZN.3, 4O0.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.114, A:L.206, A:F.221, A:Y.253, A:Y.253, A:Y.253 Hydrogen bonds: A:T.156, A:N.177, A:D.258 Salt bridges: A:H.262, A:H.306, A:H.421

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: K.27, S.28, S.223, V.224, V.225 Ligands: 4O0.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.224, A:V.225 GOL.10: 11 residues within 4Å: Chain A: N.457, V.458, D.461, T.473, H.474, G.475, S.476, L.477, N.478, L.481, N.484 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.461, A:G.475, A:G.475, A:S.476, A:L.477 Water bridges: A:N.457, A:T.473 GOL.11: 4 residues within 4Å: Chain A: G.173, N.384, R.385, R.386 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.384, A:R.386 Water bridges: A:E.170, A:R.386, A:R.386 GOL.12: 8 residues within 4Å: Chain A: I.355, T.359, K.368, P.369, Y.370, R.745, E.749, E.750 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.374, A:R.745, A:R.745 GOL.13: 6 residues within 4Å: Chain A: V.394, E.395, R.396, D.424, V.427, M.768 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.396, A:D.424, A:D.424 GOL.14: 5 residues within 4Å: Chain A: Y.670, R.674, S.738, H.803, Y.805 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.674, A:S.738, A:H.803 Water bridges: A:S.739 GOL.15: 6 residues within 4Å: Chain A: W.207, T.211, A.217, G.218, T.219, F.220 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.211, A:T.211, A:F.220 Water bridges: A:E.14, A:E.14, A:T.219, A:F.221, A:F.221

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

CL.16: 5 residues within 4Å: Chain A: K.155, G.176, N.177, S.178, R.338 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stein, A.J. et al., Structural Basis for Inhibition of Human Autotaxin by Four Potent Compounds with Distinct Modes of Binding. Mol.Pharmacol. (2015)

Release Date

2015-10-14

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2