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SMTL ID : 7g76.1

Crystal Structure of rat Autotaxin in complex with 2-[6-(4-acetylpiperazin-1-yl)-4-oxoquinazolin-3-yl]-N-[(3-chloro-4-cyanophenyl)methyl]-N-methylacetamide, i.e. SMILES O=C(C)N1CCN(CC1)c1ccc2N=CN(CC(=O)N(C)Cc3ccc(c(Cl)c3)C#N)C(=O)c2c1 with IC50=0.036628 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.1:

16 residues within 4Å:

Chain A: L.193, E.196, S.197, H.198, G.228, G.229, Q.230, 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 XWK: 2-[6-(4-acetylpiperazin-1-yl)-4-oxoquinazolin-3(4H)-yl]-N-[(3-chloro-4-cyanophenyl)methyl]-N-methylacetamide(Non-covalent)

XWK.2:

17 residues within 4Å:

Chain A: L.51, S.54, Y.55, F.183, L.186, Y.187, A.190, K.221, F.222, H.224, W.227, W.233, T.245, F.246, F.247, W.248, Y.279

14 PLIP interactions:

14 interactions with chain A

Hydrophobic interactions: A:L.51, A:Y.55, A:L.186, A:L.186, A:F.222, A:F.222, A:W.227, A:F.246, A:F.247, A:F.247, A:F.247
Hydrogen bonds: A:S.54, A:W.248
pi-Cation interactions: A:K.221

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

CL.3:

4 residues within 4Å:

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

Ligand excluded by PLIP

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

ACT.4:	5 residues within 4Å: Chain A: V.420, D.421, R.422, D.450, V.453 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.450, A:V.453 Hydrogen bonds: A:R.422 Water bridges: A:K.452 Salt bridges: A:R.422
ACT.5:	7 residues within 4Å: Chain A: T.182, N.203, L.216, D.284, H.288, H.447 Ligands: ZN.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.216 Hydrogen bonds: A:T.182, A:N.203 Salt bridges: A:K.181, A:H.288, A:H.447
ACT.6:	4 residues within 4Å: Chain A: Y.642, M.648, S.649 Ligands: K.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.682

1 x ZN: ZINC ION(Non-covalent)

ZN.7:

4 residues within 4Å:

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

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:S.777

1 x CA: CALCIUM ION(Non-covalent)

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.18

1 x K: POTASSIUM ION(Non-covalent)

K.10:

4 residues within 4Å:

Chain A: Y.642, D.645, M.648
Ligands: ACT.6

6 PLIP interactions:

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

Metal complexes: A:Y.642, A:D.645, A:M.648, ACT.6, H₂O.20, H₂O.24

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

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NGLPV2D

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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