Structure of PDB 6aui Chain A Binding Site BS02

Receptor Information
>6aui Chain A (length=745) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMHVIKRDGRQERVMFDKITSRIQKLCYGLNMDFVDPAQITMKVIQGLY
SGVTTVELDTLAAETAATLTTKHPDYAILAARIAVSNLHKETKKVFSDVM
EDLYNYINPHNGKHSPMVAKSTLDIVLANKDRLNSAIIYDRDFSYNYFGF
KTLERSYLLKINGKVAERPQHMLMRVSVGIHKEDIDAAIETYNLLSERWF
THASPTLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCALISKSAGGI
GVAVSCIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQGGNKRPGAFA
IYLEPWHLDIFEFLDLKKNTGKEEQRARDLFFALWIPDLFMKRVETNQDW
SLMCPNECPGLDEVWGEEFEKLYASYEKQGRVRKVVKAQQLWYAIIESQT
ETGTPYMLYKDSCNRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLAS
LALNMYVTSEHTYDFKKLAEVTKVVVRNLNKIIDINYYPVPEACLSNKRH
RPIGIGVQGLADAFILMRYPFESAEAQLLNKQIFETIYYGALEASCDLAK
EQGPYETYEGSPVSKGILQYDMWNVTPTDLWDWKVLKEKIAKYGIRNSLL
IAPMPTASTAQILGNNESIEPYTSNIYTRRVLSGEFQIVNPHLLKDLTER
GLWHEEMKNQIIACNGSIQSIPEIPDDLKQLYKTVWEISQKTVLKMAAER
GAFIDQSQSLNIHIAEPNYGKLTSMHFYGWKQGLKTGMYYLRTRP
Ligand information
Ligand IDDTP
InChIInChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeySUYVUBYJARFZHO-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H16 N5 O12 P3
Name2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL335538
DrugBankDB03222
ZINCZINC000008215662
PDB chain6aui Chain A Residue 803 [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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PDB6aui 3.3- angstrom resolution cryo-EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		D226 S227 R256 A263 G264
Binding residue
(residue number reindexed from 1)		D228 S229 R258 A265 G266
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) C220 N429 C431 E433 C446 Y739 Y740
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
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Biological Process
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Cellular Component
External links
PDB RCSB:6aui, PDBe:6aui, PDBj:6aui
PDBsum6aui
PubMed29460780
UniProtP23921|RIR1_HUMAN Ribonucleoside-diphosphate reductase large subunit (Gene Name=RRM1)

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