Structure of PDB 3hne Chain B Binding Site BS02

Receptor Information
>3hne Chain B (length=724) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHVIKRDGRQERVMFDKITSRIQKLCYGLNMDFVDPAQITMKVIQGLYSG
VTTVELDTLAAETAATLTTKHPDYAILAARIAVSNLHKETKKVFSDVMED
LYNYINPHNGKHSPMVAKSTLDIVLANKDRLNSAIIYDRDFSYNYFGFKT
LERSYLLKINGKVAERPQHMLMRVSVGIHKEDIDAAIETYNLLSERWFTH
ASPTLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCALISKSAGGIGV
AVSCIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQGGAFAIYLEPWH
LDIFEFLDLKKNRARDLFFALWIPDLFMKRVETNQDWSLMCPNECPGLDE
VWGEEFEKLYASYEKQGRVRKVVKAQQLWYAIIESQTETGTPYMLYKDSC
NRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYVTSEHTY
DFKKLAEVTKVVVRNLNKIIDINYYPVPEACLSNKRHRPIGIGVQGLADA
FILMRYPFESAEAQLLNKQIFETIYYGALEASCDLAKEQGPYETYEGSPV
SKGILQYDMWNVTPTDLWDWKVLKEKIAKYGIRNSLLIAPMPTASTAQIL
GNNESIEPYTSNIYTFQIVNPHLLKDLTERGLWHEEMKNQIIACNGSIQS
IPEIPDDLKQLYKTVWEISQKTVLKMAAERGAFIDQSQSLNIHIAEPNYG
KLTSMHFYGWKQGLKTGMYYLRTR
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain3hne Chain B Residue 807 [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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PDB3hne Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization.
Resolution3.11 Å
Binding residue
(original residue number in PDB)		V3 K5 R6 E11 M14 K17 I18 T53 L56
Binding residue
(residue number reindexed from 1)		V3 K5 R6 E11 M14 K17 I18 T53 L56
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C218 N427 C429 E431 C444 Y737 Y738
Catalytic site (residue number reindexed from 1) C218 N416 C418 E420 C433 Y719 Y720
Enzyme Commision number 1.17.4.1: ribonucleoside-diphosphate reductase.
Gene Ontology
Molecular Function
GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016491 oxidoreductase activity
GO:0017076 purine nucleotide binding
GO:0042802 identical protein binding
GO:0061731 ribonucleoside-diphosphate reductase activity
GO:0097718 disordered domain specific binding
Biological Process
GO:0000731 DNA synthesis involved in DNA repair
GO:0006206 pyrimidine nucleobase metabolic process
GO:0006264 mitochondrial DNA replication
GO:0006281 DNA repair
GO:0008584 male gonad development
GO:0009185 ribonucleoside diphosphate metabolic process
GO:0009263 deoxyribonucleotide biosynthetic process
GO:0009265 2'-deoxyribonucleotide biosynthetic process
GO:0010212 response to ionizing radiation
GO:0010971 positive regulation of G2/M transition of mitotic cell cycle
GO:0021846 cell proliferation in forebrain
GO:0051290 protein heterotetramerization
GO:0060041 retina development in camera-type eye
GO:0070318 positive regulation of G0 to G1 transition
GO:1900087 positive regulation of G1/S transition of mitotic cell cycle
Cellular Component
GO:0005635 nuclear envelope
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0005971 ribonucleoside-diphosphate reductase complex
GO:0042995 cell projection
GO:0043025 neuronal cell body

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3hne, PDBe:3hne, PDBj:3hne
PDBsum3hne
PubMed21336276
UniProtP23921|RIR1_HUMAN Ribonucleoside-diphosphate reductase large subunit (Gene Name=RRM1)

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