7G3N
Crystal Structure of rat Autotaxin in complex with [2-[[(2R)-5-chloro-2,3-dihydro-1H-inden-2-yl]amino]pyrimidin-5-yl]-(6-hydroxy-6-methyl-1-azaspiro[3.3]heptan-1-yl)methanone, i.e. SMILES CC1(O)CC2(CCN2C(=O)c3cnc(N[C@@H]4Cc5ccc(Cl)cc5C4)nc3)C1 with IC50=0.0155951 microM
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | polymer | 846 | 97343.3 | 1 | UniProt (Q64610) Pfam (PF01033) Pfam (PF01663) Pfam (PF01223) | Rattus norvegicus (Norway rat) | E-NPP 2,Autotaxin,Extracellular lysophospholipase D,LysoPLD |
| 2 | B (B) | 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 | branched | 1397.2 | 1 | In PDB GlyTouCan (G33303XH) | |||
| 3 | C (A) | (2-{[(2S)-5-chloro-2,3-dihydro-1H-inden-2-yl]amino}pyrimidin-5-yl)[(4s,6S)-6-hydroxy-6-methyl-1-azaspiro[3.3]heptan-1-yl]methanone | non-polymer | 398.9 | 1 | Chemie (YP5) | |||
| 4 | D (A) | ZINC ION | non-polymer | 65.4 | 1 | Chemie (ZN) | |||
| 5 | E, G (A) | CALCIUM ION | non-polymer | 40.1 | 2 | Chemie (CA) | |||
| 6 | F (A) | SODIUM ION | non-polymer | 23.0 | 1 | Chemie (NA) | |||
| 7 | H (A) | POTASSIUM ION | non-polymer | 39.1 | 1 | Chemie (K) | |||
| 8 | I, J, K, L (A) | ACETATE ION | non-polymer | 59.0 | 4 | Chemie (ACT) | |||
| 9 | M (A) | water | water | 18.0 | 545 | Chemie (HOH) |
Sequence modifications
A: 28 - 862 (UniProt: Q64610)
| PDB | External Database | Details |
|---|---|---|
| Ala 53 | Asn 53 | engineered mutation |
| Ala 410 | Asn 410 | engineered mutation |
| Thr 591 | Arg 591 | engineered mutation |
| Gly 863 | - | expression tag |
| Gly 864 | - | expression tag |
| Arg 865 | - | expression tag |
| His 866 | - | expression tag |
| His 867 | - | expression tag |
| His 868 | - | expression tag |
| His 869 | - | expression tag |
| His 870 | - | expression tag |
| His 871 | - | expression tag |
| His 872 | - | expression tag |
| His 873 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 1 |
| Total formula weight | 97343.3 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 1397.2 | |
| Non-Polymers* | Number of molecules | 10 |
| Total formula weight | 842.7 | |
| All* | Total formula weight | 99583.3 |
