5M0D
Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2,Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | polymer | 827 | 95037.7 | 1 | UniProt (Q64610) Pfam (PF01033) Pfam (PF01663) Pfam (PF01223) In PDB | Rattus norvegicus (Rat) | E-NPP 2,Autotaxin,Extracellular lysophospholipase D,LysoPLD,E-NPP 2,Autotaxin,Extracellular lysophospholipase D,LysoPLD |
| 2 | B | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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 (G34499SX) | |||
| 3 | A | IODIDE ION | non-polymer | 126.9 | 9 | Chemie (IOD) | |||
| 4 | A | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
| 5 | A | CALCIUM ION | non-polymer | 40.1 | 1 | Chemie (CA) | |||
| 6 | A | [3,5-bis(chloranyl)phenyl]methyl 4-[(4~{R})-4-[(3~{R},5~{S},7~{S},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3,7-bis(oxidanyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentyl]piperazine-1-carboxylate | non-polymer | 649.7 | 1 | Chemie (7C8) | |||
| 7 | A | SODIUM ION | non-polymer | 23.0 | 1 | Chemie (NA) | |||
| 8 | A | THIOCYANATE ION | non-polymer | 58.1 | 4 | Chemie (SCN) | |||
| 9 | A | GLYCEROL | non-polymer | 92.1 | 3 | Chemie (GOL) | |||
| 10 | water | water | 18.0 | 19 | Chemie (HOH) |
Sequence modifications
A: 36 - 591 (UniProt: Q64610)
A: 592 - 862 (UniProt: Q64610)
| PDB | External Database | Details |
|---|---|---|
| Ala 410 | Asn 410 | engineered mutation |
| Phe 581 | Leu 581 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Ala 806 | Asn 806 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 1 |
| Total formula weight | 95037.7 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 1397.2 | |
| Non-Polymers* | Number of molecules | 21 |
| Total formula weight | 2494.4 | |
| All* | Total formula weight | 98929.3 |
