SMTL ID : 9fxy.1

Crystal Structure of Autotaxin (ENPP2) with Type IV Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 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.1: 14 residues within 4Å: Chain A: L.165, Y.166, E.168, S.169, G.201, H.378, P.467, N.468, N.469, D.688, G.689, L.690, H.776 Ligands: SCN.13 No protein-ligand interaction detected (PLIP)

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

SCN.2: 7 residues within 4Å: Chain A: Y.497, P.498, H.531, I.556, L.557, Y.558, R.602 Ligand excluded by PLIP SCN.3: 7 residues within 4Å: Chain A: I.589, G.623, F.624, Y.629, W.657, A.658, Q.661 Ligand excluded by PLIP SCN.4: 6 residues within 4Å: Chain A: L.571, S.608, N.610, S.704, S.705, I.706 Ligand excluded by PLIP SCN.11: 4 residues within 4Å: Chain A: P.486, S.789, Y.790, S.791 Ligand excluded by PLIP SCN.13: 8 residues within 4Å: Chain A: E.168, H.378, A.380, N.381, Y.687, D.688, G.689 Ligands: NAG-NAG-BMA.1 Ligand excluded by PLIP SCN.14: 6 residues within 4Å: Chain A: F.105, V.106, R.107, P.109, R.244, S.246 Ligand excluded by PLIP SCN.15: 7 residues within 4Å: Chain A: T.471, H.472, F.484, P.486, T.487, Y.790, L.794 Ligand excluded by PLIP SCN.16: 6 residues within 4Å: Chain A: L.23, S.26, F.194, S.221, V.222 Ligands: 01.10 Ligand excluded by PLIP SCN.17: 3 residues within 4Å: Chain A: P.144, Y.145, P.447 Ligand excluded by PLIP SCN.18: 3 residues within 4Å: Chain A: P.634, E.635, Y.638 Ligand excluded by PLIP SCN.19: 7 residues within 4Å: Chain A: Y.159, W.199, G.201, Q.202, P.203, I.206 Ligands: 01.10 Ligand excluded by PLIP SCN.20: 1 residues within 4Å: Chain A: R.383 Ligand excluded by PLIP SCN.21: 5 residues within 4Å: Chain A: Y.668, R.672, I.716, S.736, Y.803 Ligand excluded by PLIP SCN.22: 4 residues within 4Å: Chain A: F.507, L.509, C.511, P.599 Ligand excluded by PLIP SCN.23: 3 residues within 4Å: Chain A: F.194, N.195, H.196 Ligand excluded by PLIP SCN.24: 6 residues within 4Å: Chain A: Q.202, T.207, K.210, Q.211, K.464, A.466 Ligand excluded by PLIP SCN.25: 7 residues within 4Å: Chain A: L.542, Y.543, A.726, D.727, K.728, C.729, L.733 Ligand excluded by PLIP SCN.26: 6 residues within 4Å: Chain A: K.440, N.476, H.477, L.479, R.480, N.482 Ligand excluded by PLIP SCN.27: 3 residues within 4Å: Chain A: K.440, Y.441, R.480 Ligand excluded by PLIP SCN.28: 8 residues within 4Å: Chain A: L.69, G.72, D.73, C.74, L.231, L.234, Q.235, Q.289 Ligand excluded by PLIP SCN.29: 4 residues within 4Å: Chain A: C.7, F.8, Q.235, W.236 Ligand excluded by PLIP SCN.30: 4 residues within 4Å: Chain A: R.43, G.44, W.45, E.46 Ligand excluded by PLIP SCN.31: 5 residues within 4Å: Chain A: E.46, N.77, H.87, K.278, Q.282 Ligand excluded by PLIP SCN.32: 4 residues within 4Å: Chain A: T.328, L.329, P.331, R.400 Ligand excluded by PLIP SCN.33: 5 residues within 4Å: Chain A: H.364, D.393, R.394, R.395, W.396 Ligand excluded by PLIP SCN.34: 6 residues within 4Å: Chain A: Y.145, R.147, P.447, Y.799, L.800, T.802 Ligand excluded by PLIP SCN.35: 8 residues within 4Å: Chain A: Y.650, Y.685, Q.699, V.708, P.709, T.710, H.742, R.743 Ligand excluded by PLIP SCN.36: 5 residues within 4Å: Chain A: C.750, N.751, S.752, S.753, E.754 Ligand excluded by PLIP SCN.37: 5 residues within 4Å: Chain A: K.582, S.670, E.671, N.673, F.722 Ligand excluded by PLIP SCN.38: 5 residues within 4Å: Chain A: L.720, S.734, V.735, L.796, Y.799 Ligand excluded by PLIP SCN.39: 5 residues within 4Å: Chain A: V.55, R.56, S.65, E.66, D.67 Ligand excluded by PLIP SCN.41: 6 residues within 4Å: Chain A: R.539, D.561, F.626, L.630, S.631, S.632 Ligand excluded by PLIP SCN.42: 4 residues within 4Å: Chain A: P.651, K.654, R.655 Ligands: SCN.44 Ligand excluded by PLIP SCN.43: 6 residues within 4Å: Chain A: C.511, T.512, N.595, V.597, C.611, Y.622 Ligand excluded by PLIP SCN.44: 4 residues within 4Å: Chain A: S.621, P.651, K.654 Ligands: SCN.42 Ligand excluded by PLIP SCN.45: 4 residues within 4Å: Chain A: R.119, S.121, K.124, N.426 Ligand excluded by PLIP SCN.46: 7 residues within 4Å: Chain A: Y.145, R.147, K.424, N.426, Q.429, T.802, E.804 Ligand excluded by PLIP SCN.47: 7 residues within 4Å: Chain A: H.170, G.171, F.182, R.197, W.198, G.200, R.384 Ligand excluded by PLIP SCN.49: 4 residues within 4Å: Chain A: V.492, S.493, R.494, T.552 Ligand excluded by PLIP SCN.56: 1 residues within 4Å: Chain A: K.97 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: D.256, H.260, H.304, M.306, H.419 Ligands: PO4.48 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.256, A:D.256, A:H.260, A:H.419 ZN.6: 7 residues within 4Å: Chain A: D.116, G.117, T.154, D.303, H.304, H.419 Ligands: PO4.48 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.116, A:D.116, A:T.154, A:D.303, A:H.304

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: D.684, N.686, D.688, L.690, R.691, D.692 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.684, A:D.688, A:L.690, A:D.692, H2O.6

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

IOD.8: 7 residues within 4Å: Chain A: K.153, G.174, N.175, S.176, V.330, L.334, R.336 Ligand excluded by PLIP IOD.9: 6 residues within 4Å: Chain A: T.579, S.581, G.674, P.725, A.726, D.727 Ligand excluded by PLIP IOD.12: 6 residues within 4Å: Chain A: S.176, M.177, Y.178, H.187, V.330, R.338 Ligand excluded by PLIP IOD.52: 2 residues within 4Å: Chain A: P.99, P.108 Ligand excluded by PLIP IOD.53: 4 residues within 4Å: Chain A: K.25, S.221, V.222, S.223 Ligand excluded by PLIP IOD.54: 5 residues within 4Å: Chain A: H.226, F.250, S.252, I.276, T.279 Ligand excluded by PLIP IOD.55: 3 residues within 4Å: Chain A: P.590, E.591, H.592 Ligand excluded by PLIP

1 x 01: 3-(3-((4-(4-fluorophenyl)thiazol-2-yl)(methyl)amino)-6-(1-(methylsulfonyl)piperidin-4-yl)imidazo[1,2-b]pyridazin-2-yl)propanenitrile

01.10: 24 residues within 4Å: Chain A: L.23, I.112, S.114, T.154, F.155, L.158, Y.159, L.161, A.162, K.193, F.194, H.196, W.199, P.203, W.205, I.206, F.218, F.219, W.220, A.249, Y.251, M.457 Ligands: SCN.16, SCN.19 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.112, A:F.155, A:L.158, A:L.161, A:F.194, A:W.199, A:F.219, A:A.249, A:Y.251 Hydrogen bonds: A:Y.159, A:W.205, A:W.220 Water bridges: A:R.229 pi-Stacking: A:F.218

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.40: 12 residues within 4Å: Chain A: E.452, N.455, V.456, D.459, T.471, H.472, G.473, S.474, L.475, N.476, L.479, N.482 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.455, A:D.459, A:G.473, A:S.474, A:L.475, A:N.476, A:N.476 Water bridges: A:T.471, A:S.474, A:N.476 GOL.50: 10 residues within 4Å: Chain A: R.376, L.391, V.392, D.393, R.394, F.421, D.422, K.424, V.425, M.766 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.394, A:K.424 GOL.51: 8 residues within 4Å: Chain A: I.353, T.357, K.366, P.367, Y.368, H.372, D.747, E.748 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.747 Water bridges: A:H.372, A:H.372, A:D.747, A:E.748

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.48: 11 residues within 4Å: Chain A: D.116, K.153, T.154, N.175, L.188, D.256, H.260, H.304, H.419 Ligands: ZN.5, ZN.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.154, A:N.175, A:H.304 Salt bridges: A:H.260, A:H.419

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Desroy, N. et al., Design, Synthesis, and Biological Implications of Autotaxin inhibitors with a Three-Point lock binding mode. Bioorg.Med.Chem. (2025)

Release Date

2025-04-23

Peptides

Isoform 2 of Autotaxin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoform 2 of Autotaxin

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