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SMTL ID : 7g7a.1

Crystal Structure of rat Autotaxin in complex with 2-(4-chlorophenyl)-7-methyl-8-pentylimidazo[1,2-a]pyrimidin-5-one, i.e. SMILES O=C1N2C=C(c3ccc(Cl)cc3)N=C2N(C(=C1)C)CCCCC with IC50=0.0671599 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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:

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)

3 x CA: CALCIUM ION(Non-covalent)

CA.2:	5 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 Ligands: NA.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.144, A:T.182, A:D.331, A:H.332
CA.3:	3 residues within 4Å: Chain A: Y.642, D.645, M.648 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.642, A:D.645, A:M.648, H₂O.15, H₂O.18
CA.5:	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 ZN: ZINC ION(Non-covalent)

ZN.4:

4 residues within 4Å:

Chain A: D.284, H.288, H.447
Ligands: NA.10

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.16

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

CL.6:	5 residues within 4Å: Chain A: K.181, G.202, N.203, S.204, R.364 Ligand excluded by PLIP
CL.7:	3 residues within 4Å: Chain A: R.147, S.149, G.836 Ligand excluded by PLIP
CL.8:	3 residues within 4Å: Chain A: A.680, R.683, N.774 Ligand excluded by PLIP

1 x YAQ: (4S)-2-(4-chlorophenyl)-7-methyl-8-pentylimidazo[1,2-a]pyrimidin-5(8H)-one(Non-covalent)

YAQ.9:

8 residues within 4Å:

Chain A: F.183, L.186, W.227, F.246, F.247, W.248, A.277, Y.279

9 PLIP interactions:

9 interactions with chain A

Hydrophobic interactions: A:F.183, A:W.227, A:F.246, A:F.247, A:F.247, A:A.277
Hydrogen bonds: A:W.248
pi-Stacking: A:F.247, A:Y.279

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

NA.10:

5 residues within 4Å:

Chain A: T.182, N.203, H.447
Ligands: CA.2, ZN.4

3 PLIP interactions:

3 interactions with chain A

Hydrogen bonds: A:T.182, A:T.182, A:N.203

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

ACT.11:

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
Hydrogen bonds: A:R.422
Water bridges: A:K.452
Salt bridges: A:R.422, A:K.452

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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