Structure of PDB 7mdi Chain A Binding Site BS01

Receptor Information
>7mdi Chain A (length=734) Species: 242231 (Neisseria gonorrhoeae FA 1090) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDLKVTKRDGRLEAIDLDKIHRVVTWAAEGLENVSVSQVELKSHIQFYNG
IRTDDIHETIIKAAADLISEDTPDYQYLAARLAIFHLRKIAYGEYEPPHL
YNHVKKLTDAGKYDRHILEDYSREEFDELNAYIDHERDMSFSYAAVKQLE
GKYLVQNRVTRQIYETPQFLYVLVAMCLFSKYPKEARLDYVKRFYDAVST
FKVSLPTPIMSGVRTPTRQFSSCVLIECDDSLDSINATTSAIVKYVSQRA
GIGINAGRIRGLDSEIRGGEARHTGCIPFFKMFQAAVKSCSQGGVRGGAA
TLFYPLWHIEAESLLVLKNNRGVEDNRIRQLDYGVQINRLLYTRLIKGGN
ITLFSPNEVSGLYEAFFADQDEFERLYTKYEQDPNIRKRIIPAADLFSTL
MQERAGTGRIYIQNVDHCNTHSPFDPRVAPVHQSNLCMEIALPTKPLDNI
NDPDGEIALCTLSAFNLGALNSLDELEGLADLTVRALDALLDYQGYPVEA
ARTSTMDRRSLGIGVINYAYYLAKNGVRYSDGSALGLTHRTFEAIQYYLL
KASANLAKEYGACTLFNQTVYSQGKLPIDTYKKDLDAVCGEPLHYDWESL
RADIVKYGLRNSTLTALMPSETSSQIANATNGIEPPRGLVTVKASKDGIL
KQVVPEFETLKNAYETLWQLPGNEGYLKLVGVMQKFVDQAISANTAYDPG
KFEGNKVSMKQMLKDLLTAYKYGVKTLYYHNTRD
Ligand information
Ligand IDCDP
InChIInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyZWIADYZPOWUWEW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[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)[CH](O)[CH]2O
FormulaC9 H15 N3 O11 P2
NameCYTIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL425252
DrugBankDB04555
ZINCZINC000008215624
PDB chain7mdi Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7mdi Effects of chameleon dispense-to-plunge speed on particle concentration, complex formation, and final resolution: A case study using the Neisseria gonorrhoeae ribonucleotide reductase inactive complex.
Resolution4.3 Å
Binding residue
(original residue number in PDB)		P210 T211 C227 R300 L440 C441 S624 E625 T626 S627
Binding residue
(residue number reindexed from 1)		P206 T207 C223 R296 L436 C437 S620 E621 T622 S623
Annotation score1
Enzymatic activity
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:0005524 ATP binding
GO:0016491 oxidoreductase activity
Biological Process
GO:0009263 deoxyribonucleotide biosynthetic process
Cellular Component
GO:0005971 ribonucleoside-diphosphate reductase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7mdi, PDBe:7mdi, PDBj:7mdi
PDBsum7mdi
PubMed34906669
UniProtQ5F8Z6

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