Structure of PDB 3d5x Chain A Binding Site BS01

Receptor Information

>3d5x Chain A (length=279) Species: 7955 (Danio rerio)

KEIPDVLVDPRTMKRYMRGRFLGKGGFAKCYEITDMDTKEVFAGKVVPKS
MLLKPHQKEKMSTEIAIHKSLDNPHVVGFHGFFEDDDFVYVVLEICRRRS
LLELHKRRKAVTEPEARYFMRQTIQGVQYLHNNRVIHRDLKLGNLFLNDD
MDVKIGDFGLATKIEFDGERKKDIAPEVLCKKGHSFEVDIWSLGCILYTL
LVGKPPFETSCLKETYIRIKKNEYSVPRHINPVASALIRRMLHADPTLRP
SVAELLTDEFFTSGYAPMRLPTSCLTVPP

Ligand information

• Ligand ID: KWT
• InChI: InChI=1S/C23H24O8/c1-10(24)30-13-7-22(2)12(5-6-14(22)25)16-18(13)23(3)15(9-28-4)31-21(27)11-8-29-20(17(11)23)19(16)26/h8,12-13,15H,5-7,9H2,1-4H3/t12-,13+,15+,22-,23-/m0/s1
• InChIKey: QDLHCMPXEPAAMD-QAIWCSMKSA-N
• SMILES:
  ACDLabs 10.04: O=C3c2occ1C(=O)OC(C(c12)(C5=C3C4C(C(=O)CC4)(C)CC5OC(=O)C)C)COC
  CACTVS 3.341: COC[CH]1OC(=O)c2coc3C(=O)C4=C([CH](C[C]5(C)[CH]4CCC5=O)OC(C)=O)[C]1(C)c23
  OpenEye OEToolkits 1.5.0: CC(=O)O[C@@H]1C[C@]2([C@@H](CCC2=O)C3=C1[C@@]4(c5c(coc5C3=O)C(=O)O[C@@H]4COC)C)C
  CACTVS 3.341: COC[C@H]1OC(=O)c2coc3C(=O)C4=C([C@@H](C[C@@]5(C)[C@H]4CCC5=O)OC(C)=O)[C@]1(C)c23
  OpenEye OEToolkits 1.5.0: CC(=O)OC1CC2(C(CCC2=O)C3=C1C4(c5c(coc5C3=O)C(=O)OC4COC)C)C
• Formula: C23 H24 O8
• Name: (1S,6BR,9AS,11R,11BR)-9A,11B-DIMETHYL-1-[(METHYLOXY)METHYL]-3,6,9-TRIOXO-1,6,6B,7,8,9,9A,10,11,11B-DECAHYDRO-3H-FURO[4, 3,2-DE]INDENO[4,5-H][2]BENZOPYRAN-11-YL ACETATE;
  [1S-(1A,6BA,9AB,11A,11BB)]-11-(ACETYLOXY)-1,6B,7,8,9A,10,11,11B-OCTAHYDRO-1-(METHOXYMETHLY) -9A,11B-DIMETHYL-3H-FURO[4,3,2-DE]INDENL[4,5-H]-2-BENZOPYRAN-3,6,9,TRIONE;
  WORTMANNIN
• ChEMBL: CHEMBL428496
• DrugBank: DB08059
• ZINC: ZINC000001619592
• PDB chain: 3d5x Chain A Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3d5x Structures of the wild-type and activated catalytic domains of Brachydanio rerio Polo-like kinase 1 (Plk1): changes in the active-site conformation and interactions with ligands.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): G48 A51 C53 K68 V100 C119 F169
• Binding residue (residue number reindexed from 1): G25 A28 C30 K45 V77 C96 F146
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D162 K164 G166 N167 D180
• Catalytic site (residue number reindexed from 1): D139 K141 G143 N144 D157
• Enzyme Commision number: 2.7.11.21: polo kinase.

Gene Ontology

Molecular Function

• GO:0004672 protein kinase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006468 protein phosphorylation

External links

• PDB: RCSB:3d5x, PDBe:3d5x, PDBj:3d5x
• PDBsum: 3d5x
• PubMed: 18703838
• UniProt: Q4KMI8