Structure of PDB 5kox Chain A Binding Site BS02

Receptor Information
>5kox Chain A (length=473) Species: 37329 (Nocardia farcinica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIDVIIAGGGPTGLMLAGELRLHGVRTVVLEKEPTPNQHSRSRGLHARSI
EVMDQRGLLERFLAHGEQFRVGGFFAGLAAEWPADLDTAHSYVLAIPQVV
TERLLTEHATELGAEIRRGCEVAGLDQDADGVTAELADGTRLRARYLVGC
DGGRSTVRRLLGVDFPGEPTRVETLLADVRIDVPVETLTAVVAEVRKTQL
RFGAVPAGDGFFRLIVPAQGLSADRAAPTLDELKRCLHATAGTDFGVHSP
RWLSRFGDATRLAERYRTGRVLLAGDAAHIHPPTGGQGLNLGIQDAFNLG
WKLAAAIGGWAPPDLLDSYHDERHPVAAEVLDNTRAQMTLLSLDPGPRAV
RRLMAELVEFPDVNRHLIEKITAIAVRYDLGDGHDLVGRRLRDIPLTEGR
LYERMRGGRGLLLDRTGRLSVSGWSDRVDHLADPGAALDVPAALLRPDGH
VAWVGEDQDDLLAHLPRWFGAAT
Ligand information
Ligand IDRFP
InChIInChI=1S/C43H58N4O12/c1-21-12-11-13-22(2)42(55)45-33-28(20-44-47-17-15-46(9)16-18-47)37(52)30-31(38(33)53)36(51)26(6)40-32(30)41(54)43(8,59-40)57-19-14-29(56-10)23(3)39(58-27(7)48)25(5)35(50)24(4)34(21)49/h11-14,19-21,23-25,29,34-35,39,49-53H,15-18H2,1-10H3,(H,45,55)/b12-11+,19-14+,22-13-,44-20+/t21-,23+,24+,25+,29-,34-,35+,39+,43-/m0/s1
InChIKeyJQXXHWHPUNPDRT-WLSIYKJHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](C=C\C=C(/C(=O)Nc(c2O)c(c3O)\C=N\N5CCN(CC5)C)\C)C)O)C)O)C)OC(=O)C)C)OC)C)O
ACDLabs 10.04O=C4c5c2c(O)c(\C=N\N1CCN(C)CC1)c3c(O)c2c(O)c(c5OC4(OC=CC(OC)C(C(OC(=O)C)C(C)C(O)C(C)C(O)C(C=CC=C(C(=O)N3)C)C)C)C)C
CACTVS 3.341CO[CH]1C=CO[C]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)C(=CC=C[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]1C)C)c(C=NN5CCN(C)CC5)c(O)c4c3C2=O
CACTVS 3.341CO[C@H]1\C=C\O[C@@]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)\C(=C/C=C/[C@H](C)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)C)c(\C=N\N5CCN(C)CC5)c(O)c4c3C2=O
OpenEye OEToolkits 1.5.0Cc1c(c2c3c4c1OC(C4=O)(OC=CC(C(C(C(C(C(C(C(C=CC=C(C(=O)Nc(c2O)c(c3O)C=NN5CCN(CC5)C)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
FormulaC43 H58 N4 O12
NameRIFAMPICIN
ChEMBLCHEMBL374478
DrugBankDB01045
ZINCZINC000169621223
PDB chain5kox Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5kox The Structure of the Antibiotic Deactivating, N-hydroxylating Rifampicin Monooxygenase.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		R43 G44 F69 F74 G203 V205 I215 F256 P283 T284 G285 G286
Binding residue
(residue number reindexed from 1)		R43 G44 F69 F74 G203 V205 I215 F256 P283 T284 G285 G286
Annotation score5
Binding affinityMOAD: Kd=13uM
Enzymatic activity
Catalytic site (original residue number in PDB) R43 Q68 A207 I215 P283
Catalytic site (residue number reindexed from 1) R43 Q68 A207 I215 P283
Enzyme Commision number 1.14.13.211: rifampicin monooxygenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004497 monooxygenase activity
GO:0016491 oxidoreductase activity
GO:0016709 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
GO:0071949 FAD binding

View graph for
Molecular Function
External links
PDB RCSB:5kox, PDBe:5kox, PDBj:5kox
PDBsum5kox
PubMed27557658
UniProtQ5YTV5|ROX_NOCFA Rifampicin monooxygenase (Gene Name=rox)

[Back to BioLiP]