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SMTL ID : 7g7j.1

Crystal Structure of rat Autotaxin in complex with 4-[(3aR,6aR)-2-[(E)-3-[2-[(5-methyltetrazol-2-yl)methyl]-4-(trifluoromethyl)phenyl]prop-2-enoyl]-1,3,3a,4,6,6a-hexahydropyrrolo[3,4-c]pyrrole-5-carbonyl]-3-fluorobenzenesulfonamide, i.e. SMILES [C@@H]12CN(C(=O)c3c(cc(cc3)S(=O)(=O)N)F)C[C@H]1CN(C2)C(=O)/C=C/c1ccc(cc1CN1N=NC(=N1)C)C(F)(F)F with IC50=0.00194649 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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 XSB: 3-fluoro-4-[(3aR,6aS)-5-[(2E)-3-{2-[(5-methyl-2H-tetrazol-2-yl)methyl]-4-(trifluoromethyl)phenyl}prop-2-enoyl]hexahydropyrrolo[3,4-c]pyrrole-2(1H)-carbonyl]benzene-1-sulfonamide(Non-covalent)

XSB.2:

23 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.332, H.447
Ligands: CA.3, ZN.7

13 PLIP interactions:

13 interactions with chain A

Hydrophobic interactions: A:F.183, A:F.183, A:L.186, A:L.186, A:L.216, A:L.216, A:Y.279, A:Y.279
Hydrogen bonds: A:T.182, A:N.203, A:W.248, A:D.284
pi-Stacking: A:F.246

2 x CA: CALCIUM ION(Non-covalent)

CA.3:	5 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 Ligands: XSB.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.14

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

ACT.4:

6 residues within 4Å:

Chain A: V.420, D.421, 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

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

CL.5:

4 residues within 4Å:

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

Ligand excluded by PLIP

1 x K: POTASSIUM ION(Non-covalent)

K.6:	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.12, H₂O.14, H₂O.14

1 x ZN: ZINC ION(Non-covalent)

ZN.7:

4 residues within 4Å:

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