Structure of PDB 4nkt Chain A Binding Site BS01

Receptor Information
>4nkt Chain A (length=319) Species: 4896 (Schizosaccharomyces pombe) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DMSHKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVA
FGSLESGLALKNSDMDLCVLMTIALQFYEELIAEGFEGKFLQRARIPIIK
LTSDTKNGFGASFQCAIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKH
WAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKI
VDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRR
PDGYLTKQEKGWTSRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAAS
RLLNSRSYPIPYDSLFEEA
Ligand information
Ligand ID2KH
InChIInChI=1S/C9H16N3O14P3/c13-5-1-2-12(9(16)10-5)8-7(15)6(14)4(25-8)3-24-27(17,18)11-28(19,20)26-29(21,22)23/h1-2,4,6-8,14-15H,3H2,(H,10,13,16)(H2,21,22,23)(H3,11,17,18,19,20)/t4-,6-,7-,8-/m1/s1
InChIKeyOZIBFYOFLVBDIY-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.385O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
FormulaC9 H16 N3 O14 P3
Name5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
ChEMBL
DrugBank
ZINCZINC000098208190
PDB chain4nkt Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4nkt A critical switch in the enzymatic properties of the Cid1 protein deciphered from its product-bound crystal structure.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F88 S90 N171 K197 S211 Y212 H336
Binding residue
(residue number reindexed from 1)		F51 S53 N127 K153 S167 Y168 H278
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=5.97,Kd=1.08uM
Enzymatic activity
Enzyme Commision number 2.7.7.19: polynucleotide adenylyltransferase.
2.7.7.52: RNA uridylyltransferase.
External links
PDB RCSB:4nkt, PDBe:4nkt, PDBj:4nkt
PDBsum4nkt
PubMed24322298
UniProtO13833|CID1_SCHPO Terminal uridylyltransferase cid1 (Gene Name=cid1)

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