SMTL ID : 7g78.1

Crystal Structure of rat Autotaxin in complex with 2-[6-(1-acetylpiperidin-4-yl)-4-oxoquinazolin-3-yl]-N-[[4-chloro-3-(trifluoromethoxy)phenyl]methyl]-N-methylacetamide, i.e. SMILES c1(ccc2c(c1)C(=O)N(C=N2)CC(=O)N(C)Cc1cc(c(cc1)Cl)OC(F)(F)F)C1CCN(CC1)C(=O)C with IC50=0.0156427 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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-MAN-MAN-MAN-MAN.1: 15 residues within 4Å: Chain A: L.193, E.196, S.197, H.198, G.228, G.229, Q.230, H.406, N.409, N.410, P.495, N.496, N.497, L.718, H.804 No protein-ligand interaction detected (PLIP)

1 x XSF: 2-[6-(1-acetylpiperidin-4-yl)-4-oxoquinazolin-3(4H)-yl]-N-{[4-chloro-3-(trifluoromethoxy)phenyl]methyl}-N-methylacetamide(Non-covalent)

XSF.2: 14 residues within 4Å: Chain A: L.51, S.54, Y.55, S.142, F.183, L.186, K.221, F.222, H.224, W.227, F.246, F.247, W.248, Y.279 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.55, A:L.186, A:L.186, A:F.222, A:F.222, A:W.227, A:W.227, A:F.247, A:F.247, A:F.247, A:F.247 Hydrogen bonds: A:S.54, A:W.248 pi-Cation interactions: A:K.221 Halogen bonds: A:S.142, A:L.186

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

CL.3: 4 residues within 4Å: Chain A: G.202, N.203, S.204, R.364 Ligand excluded by PLIP

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: V.420, D.421, R.422, D.450, V.453 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.450 Hydrogen bonds: A:R.422 Salt bridges: A:R.422, A:K.452 ACT.5: 7 residues within 4Å: Chain A: T.182, N.203, L.216, D.284, H.288, H.447 Ligands: ZN.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.216 Hydrogen bonds: A:T.182, A:N.203 Salt bridges: A:K.181, A:H.288, A:H.447 ACT.6: 4 residues within 4Å: Chain A: Y.642, M.648, S.649 Ligands: K.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.642

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: D.284, H.288, H.447 Ligands: ACT.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447, ACT.5

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

NA.8: 4 residues within 4Å: Chain A: N.774, D.775, S.777, S.780 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.774, A:S.780 Water bridges: A:S.780

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain A: D.712, N.714, D.716, L.718, D.720 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.712, A:D.716, A:L.718, A:D.720, H2O.18

1 x K: POTASSIUM ION(Non-covalent)

K.10: 4 residues within 4Å: Chain A: Y.642, D.645, M.648 Ligands: ACT.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.642, A:D.645, A:M.648, H2O.18, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hunziker, D. et al., Crystal Structure of a rat Autotaxin complex. To be published

Release Date

2024-12-18

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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