SMTL ID : 9fxw.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 1.95 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-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.1: 17 residues within 4Å: Chain A: L.165, Y.166, E.168, S.169, G.200, G.201, H.378, N.381, N.382, P.467, N.468, N.469, D.688, G.689, L.690, H.776 Ligands: SCN.19 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: D.256, H.260, H.304, M.306, H.419 Ligands: 01.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.256, A:D.256, A:H.260, A:H.419 ZN.3: 7 residues within 4Å: Chain A: D.116, G.117, T.154, D.303, H.304, H.419 Ligands: 01.7 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.4: 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.6

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

IOD.5: 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.6: 4 residues within 4Å: Chain A: F.570, R.691, T.693, E.694 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: K.401, P.402, L.403 Ligand excluded by PLIP IOD.32: 5 residues within 4Å: Chain A: C.52, G.53, E.66, Y.78, C.82 Ligand excluded by PLIP IOD.36: 4 residues within 4Å: Chain A: P.144, K.444, P.446, P.447 Ligand excluded by PLIP IOD.37: 6 residues within 4Å: Chain A: P.732, L.733, R.788, E.792, I.793, L.796 Ligand excluded by PLIP IOD.39: 6 residues within 4Å: Chain A: T.579, S.581, G.674, P.725, A.726, D.727 Ligand excluded by PLIP IOD.45: 4 residues within 4Å: Chain A: R.394, K.424, V.425, E.804 Ligand excluded by PLIP IOD.46: 6 residues within 4Å: Chain A: P.331, G.332, H.397, V.398, A.399 Ligands: SCN.10 Ligand excluded by PLIP IOD.47: 2 residues within 4Å: Chain A: R.189, G.190 Ligand excluded by PLIP IOD.48: 5 residues within 4Å: Chain A: F.507, L.509, G.510, C.511, P.599 Ligand excluded by PLIP IOD.53: 6 residues within 4Å: Chain A: S.176, M.177, Y.178, H.187, V.330, R.338 Ligand excluded by PLIP IOD.54: 3 residues within 4Å: Chain A: H.142, P.144, K.444 Ligand excluded by PLIP IOD.55: 5 residues within 4Å: Chain A: K.25, S.26, S.221, V.222, S.223 Ligand excluded by PLIP IOD.56: 5 residues within 4Å: Chain A: H.226, F.250, S.252, I.276, T.279 Ligand excluded by PLIP

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

01.7: 32 residues within 4Å: Chain A: I.112, D.116, K.153, T.154, F.155, L.158, Y.159, L.161, A.162, N.175, L.188, 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.304, H.419, M.457 Ligands: ZN.2, ZN.3, SCN.30, SCN.57, SCN.59 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.112, A:T.154, A:F.155, A:L.158, A:L.161, A:A.162, A:L.188, A:K.193, A:F.194, A:W.199, A:F.218, A:A.249 Hydrogen bonds: A:N.175, A:W.205, A:Y.251, A:D.256, A:H.260, A:H.419 Water bridges: A:K.153, A:K.153

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

SCN.8: 5 residues within 4Å: Chain A: Q.619, Y.650, P.651, A.652, P.744 Ligand excluded by PLIP SCN.10: 7 residues within 4Å: Chain A: L.329, P.331, A.399, R.400, D.404 Ligands: SCN.11, IOD.46 Ligand excluded by PLIP SCN.11: 6 residues within 4Å: Chain A: T.328, L.329, P.331, K.340, R.400 Ligands: SCN.10 Ligand excluded by PLIP SCN.12: 4 residues within 4Å: Chain A: Y.178, R.338, A.339, S.341 Ligand excluded by PLIP SCN.13: 4 residues within 4Å: Chain A: A.184, S.185, E.192, R.197 Ligand excluded by PLIP SCN.14: 4 residues within 4Å: Chain A: Q.254, N.271, P.272, E.275 Ligand excluded by PLIP SCN.15: 8 residues within 4Å: Chain A: K.40, N.60, A.61, C.62, H.63, D.73, R.228, Q.235 Ligand excluded by PLIP SCN.16: 6 residues within 4Å: Chain A: C.7, F.8, T.232, Q.235, W.236, L.239 Ligand excluded by PLIP SCN.17: 6 residues within 4Å: Chain A: G.623, F.624, Y.629, W.657, A.658, Q.661 Ligand excluded by PLIP SCN.18: 7 residues within 4Å: Chain A: C.358, N.746, D.747, S.749, C.750, S.752, S.753 Ligand excluded by PLIP SCN.19: 5 residues within 4Å: Chain A: G.171, N.382, R.383, R.384 Ligands: NAG-NAG-BMA-MAN-MAN.1 Ligand excluded by PLIP SCN.20: 5 residues within 4Å: Chain A: S.176, H.187, L.329, V.330, P.331 Ligand excluded by PLIP SCN.21: 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.22: 3 residues within 4Å: Chain A: E.538, R.539, D.727 Ligand excluded by PLIP SCN.23: 5 residues within 4Å: Chain A: R.19, L.23, S.26, S.28, F.194 Ligand excluded by PLIP SCN.27: 2 residues within 4Å: Chain A: D.91, D.92 Ligand excluded by PLIP SCN.29: 7 residues within 4Å: Chain A: D.617, K.618, Q.619, M.620, S.621, P.651 Ligands: GOL.40 Ligand excluded by PLIP SCN.30: 4 residues within 4Å: Chain A: L.23, F.194, H.196 Ligands: 01.7 Ligand excluded by PLIP SCN.33: 7 residues within 4Å: Chain A: S.736, S.737, F.738, M.764, K.765, T.768, Y.803 Ligand excluded by PLIP SCN.34: 6 residues within 4Å: Chain A: S.757, K.758, W.759, V.760, E.761, E.762 Ligand excluded by PLIP SCN.35: 3 residues within 4Å: Chain A: E.85, S.86, K.288 Ligand excluded by PLIP SCN.41: 4 residues within 4Å: Chain A: L.549, Y.550, R.691, G.779 Ligand excluded by PLIP SCN.42: 2 residues within 4Å: Chain A: R.545, R.784 Ligand excluded by PLIP SCN.43: 7 residues within 4Å: Chain A: L.571, S.608, Q.609, N.610, S.704, S.705, I.706 Ligand excluded by PLIP SCN.44: 6 residues within 4Å: Chain A: P.180, K.370, R.383, I.385, E.386, D.387 Ligand excluded by PLIP SCN.50: 3 residues within 4Å: Chain A: I.206, T.209, K.210 Ligand excluded by PLIP SCN.51: 6 residues within 4Å: Chain A: N.476, R.485, P.486, S.789, Y.790, S.791 Ligand excluded by PLIP SCN.52: 8 residues within 4Å: Chain A: H.372, Y.650, Y.685, V.708, P.709, T.710, H.742, R.743 Ligand excluded by PLIP SCN.57: 8 residues within 4Å: Chain A: Y.159, H.196, W.199, G.201, Q.202, P.203, I.206 Ligands: 01.7 Ligand excluded by PLIP SCN.59: 6 residues within 4Å: Chain A: F.218, F.219, W.220, R.229, Y.251 Ligands: 01.7 Ligand excluded by PLIP

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 9 residues within 4Å: Chain A: I.353, T.357, K.366, P.367, Y.368, M.369, H.372, D.747, E.748 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.357 GOL.25: 13 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, F.484 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.471, A:G.473, A:S.474, A:L.475, A:L.475, A:L.475 Water bridges: A:N.455 GOL.26: 9 residues within 4Å: Chain A: W.88, D.91, D.92, C.93, E.94, K.135, H.293, R.294, Y.435 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.92, A:E.94, A:R.294, A:Y.435 Water bridges: A:W.88, A:E.94, A:Y.435 GOL.28: 11 residues within 4Å: Chain A: G.72, D.73, C.74, T.76, L.231, L.234, Q.235, S.238, G.286, Q.289, L.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.235, A:G.286, A:Q.289 Water bridges: A:G.72, A:C.74 GOL.31: 6 residues within 4Å: Chain A: P.99, C.101, F.105, V.106, R.107, P.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.107 GOL.38: 8 residues within 4Å: Chain A: N.455, P.465, A.466, P.467, N.468, G.470, T.471, H.472 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.455, A:N.468, A:G.470, A:H.472, A:H.472 GOL.40: 7 residues within 4Å: Chain A: Y.614, K.615, M.620, S.621, Y.622, K.654 Ligands: SCN.29 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.621, A:S.621 Water bridges: A:Y.614, A:D.617 GOL.49: 6 residues within 4Å: Chain A: W.205, A.215, G.216, T.217, F.218, F.219 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.216, A:F.218 Water bridges: A:W.205, A:T.209 GOL.58: 8 residues within 4Å: Chain A: S.26, Y.27, R.189, G.190, K.193, F.194, S.221, V.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.27, A:K.193, A:V.222 Water bridges: A:S.26

Links

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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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