Structure of PDB 6c0t Chain A Binding Site BS01

Receptor Information
>6c0t Chain A (length=335) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDAEAKAKYEAEAAFFANLKLSDFNIIDTLGVGGFGRVELVQLKSEESKT
FAMKILKKRHIVDTRQQEHIRSEKQIMQGAHSDFIVRLYRTFKDSKYLYM
LMEACLGGELWTILRDRGSFEDSTTRFYTACVVEAFAYLHSKGIIYRDLK
PENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHD
ISADYWSLGILMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPKKIAKN
AANLIKKLCRDNPSERLGNLKNGVKDIQKHKWFEGFNWEGLRKGTLTPPI
IPSVASPTDTSNFDSFPEDNDEPPPDDNSGWDIDF
Ligand information
Ligand IDEE4
InChIInChI=1S/C30H30FN5O5/c1-3-12-41-24-10-11-25(40-2)27(31)26(24)28(37)17-4-6-18(7-5-17)29(38)34-22-15-32-16-23(22)35-30(39)19-8-9-21-20(13-19)14-33-36-21/h4-11,13-14,22-23,32H,3,12,15-16H2,1-2H3,(H,33,36)(H,34,38)(H,35,39)/t22-,23-/m1/s1
InChIKeyAYXNTJKOINXKAJ-DHIUTWEWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCOc1ccc(c(c1C(=O)c2ccc(cc2)C(=O)N[C@@H]3CNC[C@H]3NC(=O)c4ccc5c(c4)cn[nH]5)F)OC
CACTVS 3.385CCCOc1ccc(OC)c(F)c1C(=O)c2ccc(cc2)C(=O)N[C@@H]3CNC[C@H]3NC(=O)c4ccc5[nH]ncc5c4
ACDLabs 12.01c5c(C(c1c(OCCC)ccc(c1F)OC)=O)ccc(C(=O)NC2C(CNC2)NC(=O)c3cc4c(cc3)nnc4)c5
CACTVS 3.385CCCOc1ccc(OC)c(F)c1C(=O)c2ccc(cc2)C(=O)N[CH]3CNC[CH]3NC(=O)c4ccc5[nH]ncc5c4
OpenEye OEToolkits 2.0.6CCCOc1ccc(c(c1C(=O)c2ccc(cc2)C(=O)NC3CNCC3NC(=O)c4ccc5c(c4)cn[nH]5)F)OC
FormulaC30 H30 F N5 O5
NameN-[(3R,4R)-4-{[4-(2-fluoro-3-methoxy-6-propoxybenzene-1-carbonyl)benzene-1-carbonyl]amino}pyrrolidin-3-yl]-1H-indazole-5-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6c0t Chain A Residue 701 [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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PDB6c0t Structural basis for selective inhibition of human PKG I alpha by the balanol-like compound N46.
Resolution1.98 Å
Binding residue
(original residue number in PDB)		V368 G369 G370 F371 G372 V374 A388 I406 M438 E439 A440 C441 E445 V501 D502 G504
Binding residue
(residue number reindexed from 1)		V32 G33 G34 F35 G36 V38 A52 I70 M102 E103 A104 C105 E109 V165 D166 G168
Annotation score1
Binding affinityMOAD: ic50=43.1nM
PDBbind-CN: -logKd/Ki=7.37,IC50=43.1nM
Enzymatic activity
Catalytic site (original residue number in PDB) D484 K486 N489 D502 T521
Catalytic site (residue number reindexed from 1) D148 K150 N153 D166 T185
Enzyme Commision number 2.7.11.12: cGMP-dependent protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004692 cGMP-dependent protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6c0t, PDBe:6c0t, PDBj:6c0t
PDBsum6c0t
PubMed29769318
UniProtQ13976|KGP1_HUMAN cGMP-dependent protein kinase 1 (Gene Name=PRKG1)

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