Structure of PDB 4xru Chain F Binding Site BS01

Receptor Information
>4xru Chain F (length=424) Species: 553178 (Capnocytophaga gingivalis ATCC 33624) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MILQIHSQNPHLLDLLNKNPHTDLGIYAKSLRNGQLIGNAVSAYQYDVVF
QDTRYSYLPEESNQIDFQSYCSPLVILHICNEFFKELLQEKQTYWSQQIK
WLERTRAEVDTYPCTIEVKNLYANSTWYSKGHFMMERYFKNIHITPIVGN
NLSLRVEGKSVFEAMNLLSFIAVTTHITNTYGEYTYIDDHFAQKYARILT
NIPQVPYFVFYLFIKRAIKSERQFAEIKPMFEAYFKEEGLDIDFQFTDTH
GSRMDFIVKELGMEYPILDIGCGELKYYRRFMRRNYNYSHPYFATDTDKS
VGDYAALLKERMEADNLYFFSDWTDYEYKNPVNIILTEVIEHNTPEAAEA
LVKHCLSLNFHKMIITTPNSLFNKYYFHFEWTPQEFQDFIRHCVGDTSLE
VTYCGIGDRINGETPTQAVVITRK
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain4xru Chain F Residue 501 [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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PDB4xru Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex.
Resolution3.41 Å
Binding residue
(original residue number in PDB)		G271 D296 T297 T337 V339 N343 T344 L351
Binding residue
(residue number reindexed from 1)		G271 D296 T297 T337 V339 N343 T344 L351
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.386: small RNA 2'-O-methyltransferase.
Gene Ontology
Molecular Function
GO:0008171 O-methyltransferase activity
GO:0008173 RNA methyltransferase activity
Biological Process
GO:0001510 RNA methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4xru, PDBe:4xru, PDBj:4xru
PDBsum4xru
PubMed25882814
UniProtC2M7I7

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