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SMTL ID : 7g2y.1

Crystal Structure of rat Autotaxin in complex with 2-[(R)-2-[1-[3-[2-[(5-methyltetrazol-2-yl)methyl]-4-(trifluoromethyl)phenyl]propanoyl]piperidin-4-yl]ethylsulfinyl]-1,3-thiazole-5-sulfonamide, i.e. SMILES C1(=NC=C(S(=O)(=O)N)S1)[S@](=O)CC[C@H]1CCN(C(=O)CCc2ccc(C(F)(F)F)cc2CN2N=NC(=N2)C)CC1 with IC50=0.00230987 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 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, H.406, N.409, N.410, P.495, N.496, N.497, L.718, H.804

No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.2:	5 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 Ligands: XH0.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.144, 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.17

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.14, H₂O.18, H₂O.18

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

ACT.4:

4 residues within 4Å:

Chain A: V.420, D.421, R.422, V.453

3 PLIP interactions:

3 interactions with chain A

Hydrophobic interactions: A:V.453
Hydrogen bonds: A:R.422
Salt bridges: A:R.422

1 x XH0: 2-{(R)-2-[1-(3-{2-[(5-methyl-2H-tetrazol-2-yl)methyl]-4-(trifluoromethyl)phenyl}propanoyl)piperidin-4-yl]ethanesulfinyl}-1,3-thiazole-5-sulfonamide(Non-covalent)

XH0.5:

22 residues within 4Å:

Chain A: I.140, S.142, D.144, T.182, F.183, L.186, Y.187, L.189, A.190, N.203, L.216, W.227, W.233, F.246, F.247, W.248, Y.279, D.284, H.288, H.447
Ligands: CA.2, ZN.7

9 PLIP interactions:

9 interactions with chain A

Hydrophobic interactions: A:F.183, A:L.186, A:L.186, A:F.246, A:Y.279
Hydrogen bonds: A:T.182, A:N.203, A:W.248, A:H.332

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

CL.6:

4 residues within 4Å:

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

Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.7:

4 residues within 4Å:

Chain A: D.284, H.288, H.447
Ligands: XH0.5

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

3 PLIP interactions:

3 interactions with chain A

Hydrogen bonds: A:S.777, A:S.780
Water bridges: A:S.780

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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