Structure of PDB 7qgm Chain A Binding Site BS04

Receptor Information
>7qgm Chain A (length=516) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WELTILHTNDVHSRLEQTSEDSSKCVDASRCMGGVARLFTKVQQIRRAEP
NVLLLDAGDQYQGTIWFTVYKGAEVAHFMNALRYDAMALGNHEFDNGVEG
LIEPLLKEAKFPILSANIKAKGPLASQISGLYLPYKVLPVGDEVVGIVGY
TSKETPFLSNPGTNLVFEDEITALQPEVDKLKTLNVNKIIALGHSGFEMD
KLIAQKVRGVDVVVGGHSNTFLYTGNPPSKEVPAGKYPFIVTSDDGRKVP
VVQAYAFGKYLGYLKIEFDERGNVISSHGNPILLDSSIPEDPSIKADINK
WRIKLDDYSTQELGKTIVYLDGSSQSCRFRECNMGNLICDAMINNNLRHH
VSMCILNGGGIRSPIDERNDGTITWENLAAVLPFGGTFDLVQLKGSTLKK
AFEHSVHRYGQSTGEFLQVGGIHVVYDLSRKPGDRVVKLDVLCTKCRVPS
YDPLKMDEVYKVILPNFLANGGDGFQMIKDELLRHDSGDQDINVVSTYIS
KMKVIYPAVEGRIKFS
Ligand information
Ligand IDBOI
InChIInChI=1S/C18H24ClN3O11P2/c1-21-14(20-31-8-11-2-4-12(19)5-3-11)6-7-22(18(21)25)17-16(24)15(23)13(33-17)9-32-35(29,30)10-34(26,27)28/h2-7,13,15-17,23-24H,8-10H2,1H3,(H,29,30)(H2,26,27,28)/b20-14+/t13-,15-,16-,17-/m1/s1
InChIKeyLIVNQTQAYASRSG-UEUWNTQGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=O)N(C=CC1=NOCc2ccc(Cl)cc2)[CH]3O[CH](CO[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 2.0.7CN1C(=NOCc2ccc(cc2)Cl)C=CN(C1=O)C3C(C(C(O3)COP(=O)(CP(=O)(O)O)O)O)O
OpenEye OEToolkits 2.0.7CN1/C(=N/OCc2ccc(cc2)Cl)/C=CN(C1=O)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(CP(=O)(O)O)O)O)O
CACTVS 3.385CN/1C(=O)N(C=CC/1=N/OCc2ccc(Cl)cc2)[C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC18 H24 Cl N3 O11 P2
Name[[(2~{R},3~{S},4~{R},5~{R})-5-[(4~{E})-4-[(4-chlorophenyl)methoxyimino]-3-methyl-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
ChEMBL
DrugBank
ZINC
PDB chain7qgm Chain A Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7qgm Structure-Activity Relationship of 3-Methylcytidine-5'-alpha , beta-methylenediphosphates as CD73 Inhibitors.
Resolution2.9 Å
Binding residue
(original residue number in PDB)
D85 H118 D121 L184 N186 H243 N390 R395 F417 G447 F500 D506
Binding residue
(residue number reindexed from 1)
D59 H92 D95 L158 N160 H217 N357 R362 F384 G414 F467 D473
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.3.35: thymidylate 5'-phosphatase.
3.1.3.5: 5'-nucleotidase.
3.1.3.89: 5'-deoxynucleotidase.
3.1.3.91: 7-methylguanosine nucleotidase.
3.1.3.99: IMP-specific 5'-nucleotidase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016787 hydrolase activity
GO:0016788 hydrolase activity, acting on ester bonds
GO:0046872 metal ion binding
Biological Process
GO:0009166 nucleotide catabolic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:7qgm, PDBe:7qgm, PDBj:7qgm
PDBsum7qgm
PubMed35080883
UniProtP21589|5NTD_HUMAN 5'-nucleotidase (Gene Name=NT5E)

[Back to BioLiP]