Structure of PDB 5dst Chain H Binding Site BS01

Receptor Information
>5dst Chain H (length=317) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DSYAHFGIHEEMLKDEVRTLTYRNSMYHNKHVFKDKVVLDVGSGTGILSM
FAAKAGAKKVFGIECSSISDYSEKIIKANHLDNIITIFKGKVEEVELPVE
KVDIIISEWMGYCLFYESMLNTVIFARDKWLKPGGLMFPDRAALYVVAIE
DRQYKDFKIHWWENVYGFDMTCIRDVAMKEPLVDIVDPKQVVTNACLIKE
VDIYTVKTEELSFTSAFCLQIQRNDYVHALVTYFNIEFTKCHKKMGFSTA
PDAPYTHWKQTVFYLEDYLTVRRGEEIYGTISMKPNAKNVRDLDFTVDLD
FKGQLCETSVSNDYKMR
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 chain5dst Chain H Residue 401 [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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PDB5dst Novel helical assembly in arginine methyltransferase 8
Resolution2.963 Å
Binding residue
(original residue number in PDB)		Y80 M89 R95 G119 S120 I124 L125 E141 C142 V169 M196
Binding residue
(residue number reindexed from 1)		Y3 M12 R18 G42 S43 I47 L48 E64 C65 V92 M119
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D92 E185 E194 H334
Catalytic site (residue number reindexed from 1) D15 E108 E117 H257
Enzyme Commision number 2.1.1.319: type I protein arginine methyltransferase.
Gene Ontology
Molecular Function
GO:0016274 protein-arginine N-methyltransferase activity
Biological Process
GO:0018216 peptidyl-arginine methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5dst, PDBe:5dst, PDBj:5dst
PDBsum5dst
PubMed26876602
UniProtQ9NR22|ANM8_HUMAN Protein arginine N-methyltransferase 8 (Gene Name=PRMT8)

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