Structure of PDB 6fjf Chain D Binding Site BS02

Receptor Information
>6fjf Chain D (length=422) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVY
YNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNN
WAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTL
LISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETY
CIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADL
RKLAVNMVPFPRLHFFMPGFAPLALTVPELTQQMFDSKNMMAACDPRHGR
YLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPR
GLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFT
EAESNMNDLVSEYQQYQDATAD
Ligand information
Ligand IDDKE
InChIInChI=1S/C59H64ClN6O15/c1-32-11-9-13-48(77-6)59(75)30-47(79-57(74)62-59)33(2)54-58(3,81-54)49(29-50(69)65(4)43-24-34(23-32)25-46(76-5)53(43)60)80-51(70)14-8-7-12-36-31-66(64-63-36)22-10-21-61-55(71)35-15-18-39(56(72)73)42(26-35)52-40-19-16-37(67)27-44(40)78-45-28-38(68)17-20-41(45)52/h9,11,13,15-20,24-27,31,33,47-49,54,67,75H,7-8,10,12,14,21-23,28-30H2,1-6H3,(H,61,71)(H,62,74)(H,72,73)/b13-9+,32-11+/t33-,47+,48-,49+,54+,58+,59+/m1/s1
InChIKeyLVWXDJZBXJLTEF-IMIZWMKXSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CO[CH]1C=CC=C(C)Cc2cc(OC)c(Cl)c(c2)N(C)C(=O)C[CH](OC(=O)CCCCc3cn(CCCNC(=O)c4ccc(C(O)=O)c(c4)C5=C6C=CC(=O)[CH2]=C6Oc7cc(O)ccc57)nn3)[C]8(C)O[CH]8[CH](C)[CH]9C[C]1(O)NC(=O)O9
CACTVS 3.385CO[C@@H]1\C=C\C=C(/C)Cc2cc(OC)c(Cl)c(c2)N(C)C(=O)C[C@H](OC(=O)CCCCc3cn(CCCNC(=O)c4ccc(C(O)=O)c(c4)C5=C6C=CC(=O)[CH2]=C6Oc7cc(O)ccc57)nn3)[C@]8(C)O[C@H]8[C@H](C)[C@@H]9C[C@@]1(O)NC(=O)O9
OpenEye OEToolkits 2.0.7CC1C2CC(C(C=CC=C(Cc3cc(c(c(c3)OC)Cl)N(C(=O)CC(C4(C1O4)C)OC(=O)CCCCc5cn(nn5)CCCNC(=O)c6ccc(c(c6)C7=C8C=CC(=O)[CH2]=C8Oc9c7ccc(c9)O)C(=O)O)C)C)OC)(NC(=O)O2)O
OpenEye OEToolkits 2.0.7C[C@@H]1[C@@H]2C[C@]([C@@H](/C=C/C=C(/Cc3cc(c(c(c3)OC)Cl)N(C(=O)C[C@@H]([C@]4([C@H]1O4)C)OC(=O)CCCCc5cn(nn5)CCCNC(=O)c6ccc(c(c6)C7=C8C=CC(=O)[CH2]=C8Oc9c7ccc(c9)O)C(=O)O)C)\C)OC)(NC(=O)O2)O
FormulaC59 H64 Cl N6 O15
NameFcMaytansine
ChEMBL
DrugBank
ZINC
PDB chain6fjf Chain D Residue 503 [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]
PDB6fjf A fluorescence anisotropy assay to discover and characterize ligands targeting the maytansine site of tubulin.
Resolution2.402 Å
Binding residue
(original residue number in PDB)		G100 N102 K105 T180 V181 V182 R401 F404 W407
Binding residue
(residue number reindexed from 1)		G98 N100 K103 T178 V179 V180 R382 F385 W388
Annotation score1
Binding affinityMOAD: Kd=6.8nM
PDBbind-CN: -logKd/Ki=8.17,Kd=6.8nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005200 structural constituent of cytoskeleton
GO:0005525 GTP binding
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity
Biological Process
GO:0000226 microtubule cytoskeleton organization
GO:0000278 mitotic cell cycle
GO:0007017 microtubule-based process
GO:0007399 nervous system development
GO:1902669 positive regulation of axon guidance
Cellular Component
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0015630 microtubule cytoskeleton

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6fjf, PDBe:6fjf, PDBj:6fjf
PDBsum6fjf
PubMed29844393
UniProtQ6B856|TBB2B_BOVIN Tubulin beta-2B chain (Gene Name=TUBB2B)

[Back to BioLiP]