SMTL ID : 9ftn.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 2.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: 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.1: 12 residues within 4Å: Chain A: L.165, Y.166, 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)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.256, H.260, H.304, H.419 Ligands: 01.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.256, A:D.256, A:H.260, A:H.419 ZN.3: 8 residues within 4Å: Chain A: D.116, G.117, T.154, D.256, D.303, H.304, H.419 Ligands: 01.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.116, A:T.154, A:D.303, A:H.304

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: D.684, N.686, D.688, L.690, R.691, D.692, E.696 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.1

1 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

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)-N-(2-oxo-2,3-dihydrobenzo[d]oxazol-6-yl)propenamide

01.6: 28 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, K.193, F.194, H.196, W.199, P.203, W.205, I.206, F.218, F.219, A.249, Y.251, E.253, D.256, H.260, H.419, M.457 Ligands: ZN.2, ZN.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.112, A:T.154, A:F.155, A:A.162, A:F.194, A:W.199, A:W.199, A:W.205, A:F.219, A:Y.251 Hydrogen bonds: A:N.175, A:K.193, A:W.205, A:H.260, A:H.419 pi-Stacking: A:F.218 pi-Cation interactions: A:W.199

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

SCN.7: 2 residues within 4Å: Chain A: G.1, R.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.1, A:R.6 SCN.8: 5 residues within 4Å: Chain A: Y.614, D.617, K.618, M.620, S.621 No protein-ligand interaction detected (PLIP) SCN.9: 8 residues within 4Å: Chain A: G.623, F.624, P.628, Y.629, K.654, W.657, A.658, Q.661 No protein-ligand interaction detected (PLIP) SCN.10: 9 residues within 4Å: Chain A: E.452, N.455, V.456, G.470, T.471, H.472, G.473, S.474, L.475 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.475 SCN.11: 9 residues within 4Å: Chain A: V.149, Y.150, Y.166, P.167, R.376, L.377, H.378, Y.379, N.423 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.150, A:H.378 SCN.12: 10 residues within 4Å: Chain A: L.541, L.542, Y.543, G.544, P.546, S.577, N.676, I.678, F.782, Y.783 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.783 SCN.13: 5 residues within 4Å: Chain A: A.42, R.43, N.57, E.59, N.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.57, A:E.59 SCN.14: 5 residues within 4Å: Chain A: Y.659, R.662, V.663, D.755, E.756 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.662

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 Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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