SMTL ID : 9fxu.1

Crystal Structure of Autotaxin (ENPP2) with Type VI Inhibitor, a Novel Class of Inhibitors with Three-Point Lock Binding Mode

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 13 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 No protein-ligand interaction detected (PLIP)

1 x 01: N-(2-(3-((4-(4-fluorophenyl)thiazol-2-yl)(methyl)amino)-6-(1-(methylsulfonyl)piperidin-4-yl)imidazo[1,2-b]pyridazin-2-yl)ethyl)-2-oxo-2,3-dihydrobenzo[d]oxazole-6-carboxamide

01.2: 30 residues within 4Å: Chain A: I.112, S.114, D.116, T.154, F.155, L.158, Y.159, L.161, A.162, N.175, L.188, R.189, K.193, F.194, H.196, W.199, P.203, W.205, F.218, F.219, A.249, Y.251, E.253, D.256, H.260, H.419, M.457 Ligands: ZN.3, ZN.4, SCN.10 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.112, A:T.154, A:F.155, A:L.158, A:A.162, A:L.188, A:F.194, A:W.199, A:W.199, A:F.219, A:F.219, A:A.249, A:Y.251 Hydrogen bonds: A:R.189, A:W.205, A:Y.251, A:D.256, A:H.260, A:H.419 Water bridges: A:K.153, A:H.304, A:H.304 pi-Stacking: A:F.218

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.256, H.260, H.304, M.306, H.419 Ligands: 01.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.256, A:D.256, A:H.260, A:H.419 ZN.4: 7 residues within 4Å: Chain A: D.116, G.117, T.154, D.303, H.304, H.419 Ligands: 01.2 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.5: 5 residues within 4Å: Chain A: D.684, N.686, D.688, L.690, 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.5

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

IOD.6: 7 residues within 4Å: Chain A: K.153, G.174, N.175, S.176, V.330, L.334, R.336 Ligand excluded by PLIP

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

SCN.7: 4 residues within 4Å: Chain A: L.549, Y.550, R.691, G.779 Ligand excluded by PLIP SCN.8: 5 residues within 4Å: Chain A: K.370, N.381, N.382, R.383, Y.687 Ligand excluded by PLIP SCN.9: 6 residues within 4Å: Chain A: K.25, S.28, S.29, C.30, F.34, D.35 Ligand excluded by PLIP SCN.10: 7 residues within 4Å: Chain A: L.23, S.26, F.194, W.220, S.221, V.222 Ligands: 01.2 Ligand excluded by PLIP SCN.11: 4 residues within 4Å: Chain A: G.544, R.545, R.784, K.785 Ligand excluded by PLIP SCN.12: 2 residues within 4Å: Chain A: H.196, R.197 Ligand excluded by PLIP SCN.13: 6 residues within 4Å: Chain A: Y.145, K.424, N.426, Q.429, T.802, E.804 Ligand excluded by PLIP SCN.14: 6 residues within 4Å: Chain A: N.455, A.466, P.467, N.468, G.470, H.472 Ligand excluded by PLIP SCN.16: 4 residues within 4Å: Chain A: Y.668, R.672, S.736, Y.803 Ligand excluded by PLIP SCN.17: 7 residues within 4Å: Chain A: G.623, F.624, P.628, Y.629, W.657, A.658, Q.661 Ligand excluded by PLIP SCN.18: 4 residues within 4Å: Chain A: P.446, H.477, E.792, T.795 Ligand excluded by PLIP SCN.19: 6 residues within 4Å: Chain A: L.391, D.393, R.394, D.422, V.425, M.766 Ligand excluded by PLIP SCN.21: 10 residues within 4Å: Chain A: N.455, V.456, D.459, T.471, H.472, G.473, S.474, L.475, N.476, L.479 Ligand excluded by PLIP SCN.22: 2 residues within 4Å: Chain A: G.1, R.6 Ligand excluded by PLIP SCN.23: 4 residues within 4Å: Chain A: Y.178, R.338, A.339, K.340 Ligand excluded by PLIP SCN.24: 6 residues within 4Å: Chain A: I.589, T.594, Y.622, G.623, F.624, K.654 Ligand excluded by PLIP SCN.25: 1 residues within 4Å: Chain A: T.512 Ligand excluded by PLIP SCN.26: 8 residues within 4Å: Chain A: S.736, S.737, F.738, M.764, K.765, T.768, H.801, Y.803 Ligand excluded by PLIP SCN.27: 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.28: 5 residues within 4Å: Chain A: W.199, G.201, Q.202, P.203, I.206 Ligand excluded by PLIP SCN.29: 1 residues within 4Å: Chain A: K.210 Ligand excluded by PLIP SCN.30: 9 residues within 4Å: Chain A: G.72, D.73, C.74, T.76, L.231, L.234, G.286, Q.289, L.290 Ligand excluded by PLIP SCN.31: 10 residues within 4Å: Chain A: L.557, H.559, F.562, S.564, P.573, R.602, D.639, L.642, T.644, N.645 Ligand excluded by PLIP SCN.32: 10 residues within 4Å: Chain A: H.559, T.560, D.561, F.562, F.626, S.631, A.636, K.637, D.639, A.640 Ligand excluded by PLIP SCN.33: 8 residues within 4Å: Chain A: V.149, Y.150, Y.166, P.167, E.168, L.377, H.378, Y.379 Ligand excluded by PLIP SCN.34: 5 residues within 4Å: Chain A: Q.363, H.364, F.365, K.366, D.393 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 9 residues within 4Å: Chain A: I.353, K.366, P.367, Y.368, M.369, H.372, R.743, D.747, E.748 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.369 Water bridges: A:R.743 GOL.20: 15 residues within 4Å: Chain A: E.94, E.95, I.96, C.139, G.140, T.141, G.434, Y.435, G.436, P.437, F.439, K.440, Y.441, R.442, R.480 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.96, A:T.141, A:G.436, A:F.439, A:R.480 Water bridges: A:Y.435

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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