Structure of PDB 3nj4 Chain D Binding Site BS03

Receptor Information
>3nj4 Chain D (length=430) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSASKPLKGARIAG
CLHMTVETAVLIETLVTLGAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAW
KGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLPGIRG
ISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDG
IKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQA
AMEGYEVTTMDEACQEGNIFVTTTGCIDIILGRHFEQMKDDAIVCNIGHF
DVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMG
HPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKL
NVKLTKLTEKQAQYLGMSCDGPFKPDHYRY
Ligand information
Ligand IDAFX
InChIInChI=1S/C11H10FN5O3/c12-5-4(1-18)8(19)9(20)7(5)17-3-16-6-10(13)14-2-15-11(6)17/h2-3,7,9,18,20H,1H2,(H2,13,14,15)/t7-,9+/m1/s1
InChIKeyDMGPQGOOCCLGOU-APPZFPTMSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC1=C(C(=O)C(O)C1n2c3ncnc(c3nc2)N)CO
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3[CH](O)C(=O)C(=C3F)CO
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(=O)C(=C3F)CO)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H](C(=O)C(=C3F)CO)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@H]3[C@H](O)C(=O)C(=C3F)CO
FormulaC11 H10 F N5 O3
Name(4S,5S)-4-(6-amino-9H-purin-9-yl)-3-fluoro-5-hydroxy-2-(hydroxymethyl)cyclopent-2-en-1-one
ChEMBL
DrugBank
ZINCZINC000066166914
PDB chain3nj4 Chain D Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nj4 X-ray crystal structure and binding mode analysis of human S-adenosylhomocysteine hydrolase complexed with novel mechanism-based inhibitors, haloneplanocin A analogues.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		H55 T57 E59 E156 T157 K186 D190 G352 H353 M358
Binding residue
(residue number reindexed from 1)		H53 T55 E57 E154 T155 K184 D188 G350 H351 M356
Annotation score2
Binding affinityMOAD: ic50=0.48uM
Enzymatic activity
Catalytic site (original residue number in PDB) H55 S78 S83 D131 E156 N181 K186 D190 N191 C195 H301 H353 S361 Q365
Catalytic site (residue number reindexed from 1) H53 S76 S81 D129 E154 N179 K184 D188 N189 C193 H299 H351 S359 Q363
Enzyme Commision number 3.13.2.1: adenosylhomocysteinase.
Gene Ontology
Molecular Function
GO:0004013 adenosylhomocysteinase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
Biological Process
GO:0006730 one-carbon metabolic process
GO:0033353 S-adenosylmethionine cycle
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0042470 melanosome
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3nj4, PDBe:3nj4, PDBj:3nj4
PDBsum3nj4
PubMed21226494
UniProtP23526|SAHH_HUMAN Adenosylhomocysteinase (Gene Name=AHCY)

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