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SMTL ID : 7g50.1

Crystal Structure of rat Autotaxin in complex with 3-[[2-methylsulfanyl-5-(2,4,6-trichlorobenzoyl)phenyl]methyl]-1H-pyridazin-6-one, i.e. SMILES c1(c(ccc(c1)C(=O)c1c(cc(cc1Cl)Cl)Cl)SC)CC1=NNC(=O)C=C1 with IC50=1.03291 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 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:

14 residues within 4Å:

Chain A: L.193, E.196, S.197, H.198, G.228, H.406, N.409, N.410, P.495, N.496, N.497, D.716, L.718, H.804

No protein-ligand interaction detected (PLIP)

1 x XVQ: 6-{[2-(methylsulfanyl)-5-(2,4,6-trichlorobenzoyl)phenyl]methyl}pyridazin-3(2H)-one(Non-covalent)

XVQ.2:

14 residues within 4Å:

Chain A: I.140, S.142, F.183, L.186, Y.187, K.221, F.222, W.227, W.233, F.246, F.247, W.248, A.277, Y.279

10 PLIP interactions:

10 interactions with chain A

Hydrophobic interactions: A:L.186, A:L.186, A:W.227, A:F.246, A:F.247, A:Y.279
Hydrogen bonds: A:W.248, A:W.248
pi-Stacking: A:F.183, A:Y.279

1 x K: POTASSIUM ION(Non-covalent)

K.3:	3 residues within 4Å: Chain A: Y.642, D.645, M.648 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Y.642, A:D.645, A:M.648, H₂O.10, H₂O.13, H₂O.15

1 x ZN: ZINC ION(Non-covalent)

ZN.4:

3 residues within 4Å:

Chain A: D.284, H.288, H.447

5 PLIP interactions:

4 interactions with chain A, 1 Ligand-Water interactions

Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447, H₂O.15

1 x CA: CALCIUM ION(Non-covalent)

CA.5:

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.11

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

CL.6:

5 residues within 4Å:

Chain A: K.181, G.202, N.203, S.204, R.364

Ligand excluded by PLIP

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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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