Structure of PDB 3hnd Chain B Binding Site BS03

Receptor Information
>3hnd Chain B (length=735) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HVIKRDGRQERVMFDKITSRIQKLCYGLNMDFVDPAQITMKVIQGLYVTT
VELDTLAAETAATLTTKHPDYAILAARIAVSNLHKETKKVFSDVMEDLYN
YINPHNGKHSPMVAKSTLDIVLANKDRLNSAIIYDRDFSYNYFGFKTLER
SYLLKINGKVAERPQHMLMRVSVGIHKEDIDAAIETYNLLSERWFTHASP
TLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCALISKSAGGIGVAVS
CIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQGGNKRPGAFAIYLEP
WHLDIFEFLDLKKNTGKEEQRARDLFFALWIPDLFMKRVETNQDWSLMCP
NECPGLDEVWGEEFEKLYASYEKQGRVRKVVKAQQLWYAIIESQTETGTP
YMLYKDSCNRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNM
YVTSEHTYDFKKLAEVTKVVVRNLNKIIDINYYPVPEACLSNKRHRPIGI
GVQGLADAFILMRYPFESAEAQLLNKQIFETIYYGALEASCDLAKEQGPY
ETYEGSPVSKGILQYDMWNVTPTDLWDWKVLKEKIAKYGIRNSLLIAPMP
TASTAQILGNNESIEPYTSNIYTRREFQIVNPHLLKDLTERGLWHEEMKN
QIIACNGSIQSIPEIPDDLKQLYKTVWEISQKTVLKMAAERGAFIDQSQS
LNIHIAEPNYGKLTSMHFYGWKQGLKTGMYYLRTR
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain3hnd Chain B 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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PDB3hnd Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization.
Resolution3.21 Å
Binding residue
(original residue number in PDB)		A201 S202 S217 C218 A245 G247 R293 N427 L428 C429 E431 P603 T604 A605 S606 T607
Binding residue
(residue number reindexed from 1)		A198 S199 S214 C215 A242 G244 R290 N424 L425 C426 E428 P600 T601 A602 S603 T604
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) C215 N424 C426 E428 C441 Y730 Y731
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:3hnd, PDBe:3hnd, PDBj:3hnd
PDBsum3hnd
PubMed21336276
UniProtP23921|RIR1_HUMAN Ribonucleoside-diphosphate reductase large subunit (Gene Name=RRM1)

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