Structure of PDB 2ada Chain A Binding Site BS02

Receptor Information
>2ada Chain A (length=349) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMD
KPLSLPGFLAKFDYYMPVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYS
PHLLANSKVDPMPWNQTEGDVTPDDVVDLVNQGLQEGEQAFGIKVRSILC
CMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYEG
AVKNGIHRTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLL
KENMHFEVCPWSSYLTGAWDPKTTHAVVRFKNDKANYSLNTDDPLIFKST
LDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKELLERLYREYQ
Ligand information
Ligand IDHPR
InChIInChI=1S/C10H14N4O5/c15-1-4-6(16)7(17)10(19-4)14-3-13-5-8(14)11-2-12-9(5)18/h2,4,6-7,10,13,15-17H,1,3H2,(H,11,12,18)/t4-,6-,7-,10-/m1/s1
InChIKeyZWTNXGIZBOQCAJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(c(n1)O)NCN2[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
OpenEye OEToolkits 1.5.0c1nc2c(c(n1)O)NCN2C3C(C(C(O3)CO)O)O
CACTVS 3.341OC[CH]1O[CH]([CH](O)[CH]1O)N2CNc3c(O)ncnc23
ACDLabs 10.04Oc3ncnc1c3NCN1C2OC(C(O)C2O)CO
CACTVS 3.341OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2CNc3c(O)ncnc23
FormulaC10 H14 N4 O5
Name6-HYDROXY-7,8-DIHYDRO PURINE NUCLEOSIDE
ChEMBL
DrugBankDB02472
ZINCZINC000038321449
PDB chain2ada Chain A Residue 353 [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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PDB2ada Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		H17 D19 F61 L62 F65 M155 A183 G184 H214 E217 D295 D296
Binding residue
(residue number reindexed from 1)		H14 D16 F58 L59 F62 M152 A180 G181 H211 E214 D292 D293
Annotation score2
Binding affinityMOAD: Ki~0.1pM
PDBbind-CN: -logKd/Ki=13.00,Ki=0.1pM
Enzymatic activity
Catalytic site (original residue number in PDB) H15 H17 H214 E217 H238 D295
Catalytic site (residue number reindexed from 1) H12 H14 H211 E214 H235 D292
Enzyme Commision number 3.5.4.4: adenosine deaminase.
Gene Ontology
Molecular Function
GO:0004000 adenosine deaminase activity
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0019239 deaminase activity
GO:0046872 metal ion binding
GO:0046936 2'-deoxyadenosine deaminase activity
Biological Process
GO:0000255 allantoin metabolic process
GO:0001666 response to hypoxia
GO:0001701 in utero embryonic development
GO:0001829 trophectodermal cell differentiation
GO:0001889 liver development
GO:0001890 placenta development
GO:0002314 germinal center B cell differentiation
GO:0002467 germinal center formation
GO:0002636 positive regulation of germinal center formation
GO:0002686 negative regulation of leukocyte migration
GO:0002901 mature B cell apoptotic process
GO:0002906 negative regulation of mature B cell apoptotic process
GO:0006154 adenosine catabolic process
GO:0006157 deoxyadenosine catabolic process
GO:0006196 AMP catabolic process
GO:0006915 apoptotic process
GO:0006939 smooth muscle contraction
GO:0007155 cell adhesion
GO:0009117 nucleotide metabolic process
GO:0009168 purine ribonucleoside monophosphate biosynthetic process
GO:0010460 positive regulation of heart rate
GO:0014074 response to purine-containing compound
GO:0019722 calcium-mediated signaling
GO:0030217 T cell differentiation
GO:0030324 lung development
GO:0030890 positive regulation of B cell proliferation
GO:0032261 purine nucleotide salvage
GO:0032263 GMP salvage
GO:0032264 IMP salvage
GO:0033077 T cell differentiation in thymus
GO:0033089 positive regulation of T cell differentiation in thymus
GO:0033632 regulation of cell-cell adhesion mediated by integrin
GO:0042100 B cell proliferation
GO:0042110 T cell activation
GO:0043066 negative regulation of apoptotic process
GO:0043084 penile erection
GO:0043605 amide catabolic process
GO:0044209 AMP salvage
GO:0045580 regulation of T cell differentiation
GO:0045582 positive regulation of T cell differentiation
GO:0045987 positive regulation of smooth muscle contraction
GO:0046059 dAMP catabolic process
GO:0046061 dATP catabolic process
GO:0046085 adenosine metabolic process
GO:0046101 hypoxanthine biosynthetic process
GO:0046103 inosine biosynthetic process
GO:0046111 xanthine biosynthetic process
GO:0046632 alpha-beta T cell differentiation
GO:0046638 positive regulation of alpha-beta T cell differentiation
GO:0048286 lung alveolus development
GO:0048541 Peyer's patch development
GO:0048566 embryonic digestive tract development
GO:0050728 negative regulation of inflammatory response
GO:0050850 positive regulation of calcium-mediated signaling
GO:0050852 T cell receptor signaling pathway
GO:0050862 positive regulation of T cell receptor signaling pathway
GO:0050870 positive regulation of T cell activation
GO:0050900 leukocyte migration
GO:0060169 negative regulation of adenosine receptor signaling pathway
GO:0060407 negative regulation of penile erection
GO:0070242 thymocyte apoptotic process
GO:0070244 negative regulation of thymocyte apoptotic process
GO:0070254 mucus secretion
GO:0070256 negative regulation of mucus secretion
GO:0140928 inhibition of non-skeletal tissue mineralization
Cellular Component
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0031410 cytoplasmic vesicle
GO:0060205 cytoplasmic vesicle lumen
GO:0070161 anchoring junction

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ada, PDBe:2ada, PDBj:2ada
PDBsum2ada
PubMed1925539
UniProtP03958|ADA_MOUSE Adenosine deaminase (Gene Name=Ada)

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