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SMTL ID : 7g74.1

Crystal Structure of rat Autotaxin in complex with 4-[[4-[[6-(4-acetylpiperazin-1-yl)-4-oxoquinazolin-3-yl]methyl]triazol-1-yl]methyl]-2-fluorobenzonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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:

17 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, A.494, P.495, N.496, N.497, D.716, L.718, H.804

No protein-ligand interaction detected (PLIP)

1 x Y7T: 4-[(4-{[6-(4-acetylpiperazin-1-yl)-4-oxoquinazolin-3(4H)-yl]methyl}-1H-1,2,3-triazol-1-yl)methyl]-2-fluorobenzonitrile(Non-covalent)

Y7T.2:

16 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, F.246, F.247, W.248, Y.279

9 PLIP interactions:

9 interactions with chain A

Hydrophobic interactions: A:L.51, A:Y.55, A:L.186, A:L.186, A:W.227, A:F.247
Hydrogen bonds: A:S.54, A:W.248
pi-Stacking: A:F.247

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

2 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.450, A:V.453 Hydrogen bonds: A:R.422 Salt bridges: A:R.422
ACT.5:	3 residues within 4Å: Chain A: R.165, H.170, P.172 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.172 Salt bridges: A:R.165, A:H.170

1 x ZN: ZINC ION(Non-covalent)

ZN.6:

3 residues within 4Å:

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

5 PLIP interactions:

4 interactions with chain A, 1 Ligand-Water interactions

Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447, H₂O.19

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

NA.7:

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

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.20
CA.9:	4 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 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

1 x K: POTASSIUM ION(Non-covalent)

K.10:

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.11, H₂O.22, H₂O.23

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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