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SMTL ID : 7g3k.1

Crystal Structure of rat Autotaxin in complex with 5-tert-butyl-2-chloro-4-[(7-methyl-8-oxo-5,6-dihydroimidazo[1,5-a]pyrazin-3-yl)methoxy]benzonitrile, i.e. SMILES c1c(c(cc(c1C(C)(C)C)OCC1=NC=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 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 YEL: 5-tert-butyl-2-chloro-4-{[(4S)-7-methyl-8-oxo-5,6,7,8-tetrahydroimidazo[1,5-a]pyrazin-3-yl]methoxy}benzonitrile(Non-covalent)

YEL.2:

14 residues within 4Å:

Chain A: I.140, S.142, T.182, F.183, L.186, Y.187, L.189, A.190, W.233, F.246, F.247, W.248, A.277, Y.279

7 PLIP interactions:

7 interactions with chain A

Hydrophobic interactions: A:F.183, A:L.186, A:Y.187, A:W.233, A:F.246
Hydrogen bonds: A:W.248
pi-Stacking: A:F.247

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

ACT.3:	4 residues within 4Å: Chain A: V.420, D.421, R.422, V.453 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.422 Salt bridges: A:R.422
ACT.4:	4 residues within 4Å: Chain A: Y.642, M.648, S.649 Ligands: K.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.642 Salt bridges: A:K.682
ACT.5:	8 residues within 4Å: Chain A: D.144, T.182, D.284, H.288, H.332, H.447 Ligands: ZN.6, CA.9 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.182 Salt bridges: A:H.288, A:H.332, A:H.447

1 x ZN: ZINC ION(Non-covalent)

ZN.6:

4 residues within 4Å:

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

5 PLIP interactions:

4 interactions with chain A, 1 Ligand-Ligand interactions

Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447, ACT.5

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

NA.7:

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

2 x CA: CALCIUM ION(Non-covalent)

CA.8:	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
CA.9:	5 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 Ligands: ACT.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.144, A:D.144, A:D.331, A:H.332, ACT.5

1 x K: POTASSIUM ION(Non-covalent)

K.10:

4 residues within 4Å:

Chain A: Y.642, D.645, M.648
Ligands: ACT.4

6 PLIP interactions:

3 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions

Metal complexes: A:Y.642, A:D.645, A:M.648, H₂O.3, H₂O.14, ACT.4

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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