Structure of PDB 5x22 Chain M Binding Site BS04

Receptor Information
>5x22 Chain M (length=1112) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRE
TFPIEEGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTG
LIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPG
RYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQET
LARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAY
VYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPT
LRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVR
ERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRH
KRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLA
AYARVDELGFIRTPYRRVVGGVVTDEVVYMTATEEDRYTIAQANTPLEGN
RIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDAN
RALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKV
DGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLA
DGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIE
RYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILV
GRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRL
RRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVE
DMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIF
DGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPG
KTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMH
ARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLK
SDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKD
NPVDIFEGLASK
Ligand information
Ligand ID2TM
InChIInChI=1S/C10H18N3O13P3/c11-6-1-2-13(10(16)12-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H2,11,12,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1
InChIKeySTGUOVSTMBLHFT-ZOQUXTDFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
CACTVS 3.385NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
CACTVS 3.385NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
FormulaC10 H18 N3 O13 P3
Name5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine;
CMPcPP
ChEMBL
DrugBank
ZINCZINC000098208273
PDB chain5x22 Chain N Residue 2007 [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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PDB5x22 Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase.
Resolution3.35 Å
Binding residue
(original residue number in PDB)		R557 R879
Binding residue
(residue number reindexed from 1)		R551 R873
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0006351 DNA-templated transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5x22, PDBe:5x22, PDBj:5x22
PDBsum5x22
PubMed28622509
UniProtQ8RQE9|RPOB_THET8 DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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