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SMTL ID : 7g4g.1

Crystal Structure of rat Autotaxin in complex with 7-[3-(4-acetyl-3-hydroxy-2-propylphenoxy)-2-hydroxypropoxy]-4-oxo-8-propylchromene-2-carboxylic acid, i.e. SMILES c12c(c(ccc1C(=O)C=C(O2)C(=O)O)OC[C@@H](COc1c(c(c(cc1)C(=O)C)O)CCC)O)CCC with IC50=0.249971 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 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:

15 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, G.717, L.718, H.804

No protein-ligand interaction detected (PLIP)

1 x YNN: 7-[(2R)-3-(4-acetyl-3-hydroxy-2-propylphenoxy)-2-hydroxypropoxy]-4-oxo-8-propyl-4H-1-benzopyran-2-carboxylic acid(Non-covalent)

YNN.2:

18 residues within 4Å:

Chain A: L.51, S.54, I.140, S.142, F.183, L.186, L.189, A.190, L.216, R.217, K.221, F.222, W.233, F.246, F.247, W.248, V.250, Y.279

19 PLIP interactions:

19 interactions with chain A

Hydrophobic interactions: A:L.51, A:I.140, A:F.183, A:L.186, A:L.186, A:L.186, A:L.189, A:F.222, A:F.246, A:F.246, A:F.247, A:F.247, A:Y.279, A:Y.279
Hydrogen bonds: A:W.248, A:W.248
Water bridges: A:R.257
Salt bridges: A:K.221
pi-Stacking: A:F.183

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.21

1 x K: POTASSIUM ION(Non-covalent)

K.4:	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.14, H₂O.20, H₂O.22

1 x CA: CALCIUM ION(Non-covalent)

CA.5:

6 residues within 4Å:

Chain A: D.712, N.714, D.716, L.718, R.719, 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 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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