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SMTL ID : 7g5v.1

Crystal Structure of rat Autotaxin in complex with [3-fluoro-4-(trifluoromethoxy)phenyl]methyl 4-[(1H-benzotriazole-5-carbonylamino)methyl]-4-hydroxypiperidine-1-carboxylate, i.e. SMILES C1CN(CCC1(O)CNC(=O)c1cc2c(cc1)NN=N2)C(=O)OCc1cc(c(cc1)OC(F)(F)F)F with IC50=0.00632449 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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:

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 YFT: [3-fluoro-4-(trifluoromethoxy)phenyl]methyl 4-{[(1H-benzotriazole-5-carbonyl)amino]methyl}-4-hydroxypiperidine-1-carboxylate(Non-covalent)

YFT.2:

20 residues within 4Å:

Chain A: I.140, S.142, D.144, T.182, F.183, L.186, L.189, A.190, N.203, L.216, W.233, F.246, F.247, W.248, Y.279, D.284, H.288, H.447
Ligands: CA.3, ZN.7

5 PLIP interactions:

5 interactions with chain A

Hydrophobic interactions: A:L.216, A:F.247, A:Y.279
Hydrogen bonds: A:N.203, A:W.248

2 x CA: CALCIUM ION(Non-covalent)

CA.3:	5 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 Ligands: YFT.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.144, A:T.182, A:D.331, A:H.332
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.7

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

ACT.4:	5 residues within 4Å: Chain A: V.420, R.422, D.450, K.452, V.453 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.450, A:V.453 Hydrogen bonds: A:R.422 Salt bridges: A:R.422, A:K.452
ACT.5:	5 residues within 4Å: Chain A: Y.642, M.648, S.649, Y.650 Ligands: K.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.648

1 x K: POTASSIUM ION(Non-covalent)

K.6:	4 residues within 4Å: Chain A: Y.642, D.645, M.648 Ligands: ACT.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.642, A:D.645, A:M.648, H₂O.8, H₂O.12

1 x ZN: ZINC ION(Non-covalent)

ZN.7:

4 residues within 4Å:

Chain A: D.284, H.288, H.447
Ligands: YFT.2

4 PLIP interactions:

4 interactions with chain A

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

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

NA.8:

4 residues within 4Å:

Chain A: N.774, D.775, S.777, S.780

2 PLIP interactions:

2 interactions with chain A

Hydrogen bonds: A:N.774, A:S.780

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

CL.10:

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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