Structure of PDB 6exi Chain A Binding Site BS01

Receptor Information
>6exi Chain A (length=468) Species: 29448 (Bradyrhizobium elkanii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFTDYIVKDIALADFGRKEISLAETEMPGLMATREEYGPKQPLKGARIAG
SLHMTIQTAVLIETLAALGADIRWVSCNIYSTQDHAAAAIAAAGIPVFAV
KGETLTEYWDYTAKLFDWHGGGTPNMILDDGGDATMLVHAGYRAEQGDTA
FLDKPGSEEEEIFYALVKRLLKEKPKGWFAEIAKNIKGVSEETTTGVHRL
YEMANKGTLLFPAINVNDSVTKSKFDNLYGCRESLVDGIRRGTDVMLSGK
VAMVAGFGDVGKGSAASLRQAGCRVMVSEVDPICALQAAMEGYEVVTMED
AAPRADIFVTATGNKDIITIEHMRAMKDRAIVCNIGHFDNEIQIASLRNL
KWTNIKPQVDEIEFPDKHRIIMLSEGRLVNLGNAMGHPSFVMSASFTNQT
LAQIELFANNKDSKYAKKVYVLPKTLDEKVARLHLAKIGVKLTELRKDQA
DYIGVKQEGPYKSDHYRY
Ligand information
Ligand IDADN
InChIInChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
InChIKeyOIRDTQYFTABQOQ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
FormulaC10 H13 N5 O4
NameADENOSINE
ChEMBLCHEMBL477
DrugBankDB00640
ZINCZINC000002169830
PDB chain6exi Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6exi S-Adenosyl-L-Homocysteine Hydrolase Inhibition by a Synthetic Nicotinamide Cofactor Biomimetic.
Resolution1.918 Å
Binding residue
(original residue number in PDB)		H58 T60 Q62 D231 H342 N385 L386 G391 H392 M397
Binding residue
(residue number reindexed from 1)		H53 T55 Q57 D226 H337 N380 L381 G386 H387 M392
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=5.05,Kd=9uM
Enzymatic activity
Catalytic site (original residue number in PDB) H58 S81 S86 D135 E197 N222 K227 D231 N232 C236 H342 H392 S400 Q404
Catalytic site (residue number reindexed from 1) H53 S76 S81 D130 E192 N217 K222 D226 N227 C231 H337 H387 S395 Q399
Enzyme Commision number 3.13.2.1: adenosylhomocysteinase.
Gene Ontology
Molecular Function
GO:0004013 adenosylhomocysteinase activity
GO:0016787 hydrolase activity
Biological Process
GO:0006730 one-carbon metabolic process
GO:0033353 S-adenosylmethionine cycle
GO:0071269 L-homocysteine biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6exi, PDBe:6exi, PDBj:6exi
PDBsum6exi
PubMed29619018
UniProtA0A087WNH6|SAHH_BRAEL Adenosylhomocysteinase (Gene Name=ahcY)

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