Structure of PDB 8p23 Chain B Binding Site BS01

Receptor Information
>8p23 Chain B (length=715) Species: 165179 (Segatella copri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IQTVVKRDGRIVGFNEQKIMAAIRKAMLHTDKDTTLIEQITDHISYMSVE
AIQDAIEMELMKSDVAQKYIAYRNQRNIARKAKTRDVFMSIVNAKNNDIT
RENANMNADTPAGMMMKFASETTKPFVDDYLLSEDVRDAVMHNYIHIHDK
DYYPTKSLTCVQHPLDVILNHGFRPAKRIETAAVLACISLETCQNEMHGG
QAIPAFDFYLAPYVRMSYQEEVKNLEKLTGEDLSNLYDAPIDDYIEKPLD
GLQGRERLEQHAINKTVNRVHQAMEAFIHNMNTIHSRGGNQVVFSSINYG
TDTSAEGRCIMREILQSTYQGVGNGETAIFPIQIWKKKRGVNYLPEDRNY
DLYKLACKVTARRFFPNFLNLDATFNQNEKWRADDPERYKWEIATMGCRT
RVFEDRWGEKTSIARGNLSFSTINIVKLAIECMGIENEKQRIDMFFAKLD
NILDITAKQLDERFQFQKTAMAKQFPLLMKYLWVGAENLKPEETIESVIN
HGTLGIGFIGLAECLVALIGKHHGESEKAQELGLKIITYMRDRANEFSEQ
YHHNYSILATPAEGLSGKFTKKDRKQFGVIPGVTDRDYYTNSNHVPVYYK
CTALKKAQIEAPYHDLTRGGHIFYVEIDGDATHNPSVIESVVDMMDKYNM
GYGSVNHNRNRCGYENADAHLEVCPKCGSHHIDKLQRITGYLVGTTDRWN
SGKLAELHDRVTHIG
Ligand information
Ligand IDCTP
InChIInChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPCDQPRRSZKQHHS-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
FormulaC9 H16 N3 O14 P3
NameCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL223533
DrugBankDB02431
ZINCZINC000003861746
PDB chain8p23 Chain B Residue 801 [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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PDB8p23 Activity modulation in anaerobic ribonucleotide reductase: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site
Resolution3.17 Å
Binding residue
(original residue number in PDB)		E113 H159 G217 F312 P579 A580 E581 G582
Binding residue
(residue number reindexed from 1)		E102 H148 G199 F294 P561 A562 E563 G564
Annotation score1
Enzymatic activity
Enzyme Commision number 1.17.4.2: ribonucleoside-triphosphate reductase (thioredoxin).
Gene Ontology
Molecular Function
GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0005524 ATP binding
GO:0008998 ribonucleoside-triphosphate reductase (thioredoxin) activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0006260 DNA replication
GO:0009265 2'-deoxyribonucleotide biosynthetic process
Cellular Component
GO:0031250 anaerobic ribonucleoside-triphosphate reductase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8p23, PDBe:8p23, PDBj:8p23
PDBsum8p23
PubMed38968292
UniProtA0A3E4SF67

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