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SMTL ID : 7g2z.1

Crystal Structure of rat Autotaxin in complex with 3-cyclopropyl-5-[3-ethyl-2-fluoro-6-[(4-methyl-5-oxo-1H-1,2,4-triazol-3-yl)methoxy]phenoxy]benzonitrile, i.e. SMILES N1(C(=O)NN=C1COc1c(c(c(cc1)CC)F)Oc1cc(cc(c1)C#N)C1CC1)C with IC50=0.132219 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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.1:

13 residues within 4Å:

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

No protein-ligand interaction detected (PLIP)

1 x XI4: 3-cyclopropyl-5-{3-ethyl-2-fluoro-6-[(4-methyl-5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)methoxy]phenoxy}benzonitrile(Non-covalent)

XI4.2:

11 residues within 4Å:

Chain A: F.183, L.186, A.190, K.221, F.222, W.227, W.233, F.246, F.247, W.248, Y.279

17 PLIP interactions:

17 interactions with chain A

Hydrophobic interactions: A:F.183, A:A.190, A:K.221, A:F.222, A:F.222, A:W.227, A:W.233, A:F.246, A:F.247, A:F.247, A:F.247
Hydrogen bonds: A:F.246, A:F.247, A:W.248, A:W.248
pi-Stacking: A:F.247, A:Y.279

1 x ZN: ZINC ION(Non-covalent)

ZN.3:

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.14

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

NA.4:	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
NA.6:	3 residues within 4Å: Chain A: Y.642, D.645, M.648 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.642

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.16

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

CL.7:

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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