Structure of PDB 6h9x Chain A Binding Site BS01

Receptor Information
>6h9x Chain A (length=428) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLDPNLLRTEPDAVAEKLARRGFKLDVDKLRALEERRKVLQVQTENLQAE
RNSRSKSIGQAKARDIEPLRLEVNKLGEQLDAAKSELETLLAEIRDIALA
IPNIPHDDVPVGRDENDNVEVSRWGTPRQFDFEVRDHVTLGEMHGGLDFA
AAVKLTGSRFVVMKGQLARLHRALAQFMLDLHTEQHGYSENYVPYLVNQD
TLYGTGQLPKFAGDLFHTRPLEEEADSSNYALIPTAEVPLTNLVRDEIID
EDDLPIKMTAHTPCFRSEAGSYGRDTRGLIRMHQFDKVEMVQIVRPEDSM
AALEEMTGHAEKVLQLLGLPYRKVALCTGDMGFSACKTYDLEVWVPAQNT
YREISSCSNVWDFQARRMQARCRSKSDKKTRLVHTLNGSGLAVGRTLVAL
MENYQQADGRIEIPEVLRPYMRGLEYIG
Ligand information
Ligand IDSSA
InChIInChI=1S/C13H19N7O8S/c14-5(1-21)12(24)19-29(25,26)27-2-6-8(22)9(23)13(28-6)20-4-18-7-10(15)16-3-17-11(7)20/h3-6,8-9,13,21-23H,1-2,14H2,(H,19,24)(H2,15,16,17)/t5-,6+,8+,9+,13+/m0/s1
InChIKeyHQXFJGONGJPTLZ-YTMOPEAISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CO)N)O)O)N
CACTVS 3.341N[CH](CO)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341N[C@@H](CO)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CO
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CO)N)O)O)N
FormulaC13 H19 N7 O8 S
Name5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
ChEMBLCHEMBL1163070
DrugBankDB03869
ZINCZINC000013542770
PDB chain6h9x Chain A 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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PDB6h9x Acylated sulfonamide adenosines as potent inhibitors of the adenylate-forming enzyme superfamily.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		T237 E239 R268 E270 I282 R283 M284 F287 K289 E291 E355 I356 S357 S358 N389 S391 A394 R397
Binding residue
(residue number reindexed from 1)		T235 E237 R266 E268 I280 R281 M282 F285 K287 E289 E353 I354 S355 S356 N387 S389 A392 R395
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=9.74,Ki=0.18nM
Enzymatic activity
Enzyme Commision number 6.1.1.11: serine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004828 serine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006434 seryl-tRNA aminoacylation
GO:0016260 selenocysteine biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6h9x, PDBe:6h9x, PDBj:6h9x
PDBsum6h9x
PubMed31048140
UniProtW9BNU9

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