Structure of PDB 4qdk Chain A Binding Site BS01

Receptor Information
>4qdk Chain A (length=219) Species: 1111708 (Synechocystis sp. PCC 6803 substr. Kazusa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DDKTIVRDYFNSTGFDRWRRIYGDGQVNFVQKDIRVGHQQTVDSVVAWLV
ADGNLPGLLVCDAGCGVGSLSIPLAQAGALVYGSDISEKMVGEAQQKAQE
VLAYGNQPTFMTQDLAQLGGKYDTVICLDVLIHYPTEEASAMISHLASLA
DRRLILSFAPKTLGLTVLKKIGGLFPGRAYQHKEADIRKILGDNGFSIAR
TGMTSTRFYYSRILEAVRS
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 chain4qdk Chain A Residue 301 [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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PDB4qdk Structural insights into the catalytic mechanism of Synechocystis magnesium protoporphyrin IX O-methyltransferase (ChlM).
Resolution1.7 Å
Binding residue
(original residue number in PDB)		F16 Y28 H44 G70 C71 G72 D91 I92 D120 L121 L134 Y140
Binding residue
(residue number reindexed from 1)		F10 Y22 H38 G64 C65 G66 D85 I86 D114 L115 L128 Y134
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=5.85,Kd=1.4uM
Enzymatic activity
Enzyme Commision number 2.1.1.11: magnesium protoporphyrin IX methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0046406 magnesium protoporphyrin IX methyltransferase activity
Biological Process
GO:0015979 photosynthesis
GO:0015995 chlorophyll biosynthetic process
GO:0032259 methylation
GO:0036068 light-independent chlorophyll biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4qdk, PDBe:4qdk, PDBj:4qdk
PDBsum4qdk
PubMed25077963
UniProtQ55467|CHLM_SYNY3 Magnesium-protoporphyrin O-methyltransferase (Gene Name=chlM)

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