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SMTL ID : 7g6e.1

Crystal Structure of rat Autotaxin in complex with 4-[(7-benzyl-9-methyl-8-oxopurin-2-yl)amino]-N-(1-methylpiperidin-4-yl)benzamide, i.e. SMILES N1(c2c(N(C1=O)Cc1ccccc1)cnc(n2)Nc1ccc(C(=O)NC2CCN(CC2)C)cc1)C with IC50=0.0611585 microM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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 Y2H: 4-[(7-benzyl-9-methyl-8-oxo-8,9-dihydro-7H-purin-2-yl)amino]-N-(1-methylpiperidin-4-yl)benzamide(Non-covalent)

Y2H.2:

12 residues within 4Å:

Chain A: S.142, T.182, F.183, L.186, Y.187, L.216, W.233, F.246, F.247, A.277, Y.279, D.284

9 PLIP interactions:

9 interactions with chain A

Hydrophobic interactions: A:T.182, A:F.183, A:A.277
Water bridges: A:W.248, A:W.248, A:Y.279
Salt bridges: A:D.284
pi-Stacking: A:F.246, A:F.247

1 x K: POTASSIUM ION(Non-covalent)

K.3:	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.13, H₂O.16, H₂O.17

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

4 PLIP interactions:

4 interactions with chain A

Hydrophobic interactions: A:D.450
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

2 x CA: CALCIUM ION(Non-covalent)

CA.6:	4 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.144, A:D.144, A:D.331, A:H.332, H₂O.1
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.16

1 x ZN: ZINC ION(Non-covalent)

ZN.7:

3 residues within 4Å:

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

5 PLIP interactions:

3 interactions with chain A, 2 Ligand-Water interactions

Metal complexes: A:D.284, A:H.288, A:H.447, H₂O.1, H₂O.15

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

NA.8:

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

1 x Y29: 2-(4-chloroanilino)-7,9-dimethyl-7,9-dihydro-8H-purin-8-one(Non-covalent)

Y29.10:

7 residues within 4Å:

Chain A: R.700, L.748, S.762, V.763, L.824, Y.827, H.829

5 PLIP interactions:

5 interactions with chain A

Hydrogen bonds: A:V.763, A:V.763, A:Y.827
pi-Stacking: A:Y.827, A:H.829

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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