Structure of PDB 6dmb Chain A Binding Site BS02

Receptor Information
>6dmb Chain A (length=990) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKAPLWLRAKFQRLLFKLGCYIQKNCGKFLVVGLLIFGAFAVGLKAANLE
TNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMIQTPKEEGANVLTT
EALLQHLDSALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQIIEY
LYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLRWTNFDPLEFLEELKKIN
YQVDSWEEMLNKAEVGHGYMDRPCLNPADPDCPATAPNKNSTKPLDMALV
LNGGCHGLSRKYMHWQEELIVGGTVKNSTGKLVSAHALQTMFQLMTPKQM
YEHFKGYEYVSHINWNEDKAAAILEAWQRTYVEVVHQSVAQNSTQKVLSF
TTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLRWDCSKSQGAVGLA
GVLLVALSVAAGLGLCSLIGISFNAATTQVLPFLALGVGVDDVFLLAHAF
SETGQNKRIPFEDRTGECLKRTGASVALTSISNVTAFFMAALIPIPALRA
FSLQAAVVVVFNFAMVLLIFPAILSMDLYRREDRRTLSSFAEKHYAPFLL
KPKAKVVVIFLFLGLLGVSLYGTTRVRDGLDLTDIVPRETREYDFIAAQF
KYFSFYNMYIVTQKADYPNIQHLLYDLHRSFSNVKYVMLEENKQLPKMWL
HYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDDGVLAYKLLVQTGSRDK
PIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQANIRPHR
PEWVHDKADYMPETRLRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVR
TICSNYTSLGLSSYPNGYPFLFWEQYIGLRHWLLLFISVVLACTFLVCAV
FLLNPWTAGIIVMVLALMTVELFGMMGLIGIKLSAVPVVILIASVGIGVE
FTVHVALAFLTAIGDKNRRAVLALEHMFAPVLDGAVSTLLGVLMLAGSEF
DFIVRYFFAVLAILTILGVLNGLVLLPVLLSFFGPYPEVS
Ligand information
Ligand IDY01
InChIInChI=1S/C31H50O4/c1-20(2)7-6-8-21(3)25-11-12-26-24-10-9-22-19-23(35-29(34)14-13-28(32)33)15-17-30(22,4)27(24)16-18-31(25,26)5/h9,20-21,23-27H,6-8,10-19H2,1-5H3,(H,32,33)/t21-,23+,24+,25-,26+,27+,30+,31-/m1/s1
InChIKeyWLNARFZDISHUGS-MIXBDBMTSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)OC(=O)CCC(O)=O
OpenEye OEToolkits 1.6.1CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)OC(=O)CCC(=O)O)C)C
OpenEye OEToolkits 1.6.1CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)OC(=O)CCC(=O)O)C)C
CACTVS 3.352CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](CC[C]4(C)[CH]3CC[C]12C)OC(=O)CCC(O)=O
FormulaC31 H50 O4
NameCHOLESTEROL HEMISUCCINATE
ChEMBL
DrugBank
ZINCZINC000058638837
PDB chain6dmb Chain A Residue 1809 [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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PDB6dmb Structural basis for the recognition of Sonic Hedgehog by human Patched1.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		A119 L121 V437 Y446
Binding residue
(residue number reindexed from 1)		A47 L49 V365 Y374
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005113 patched binding
GO:0005119 smoothened binding
GO:0005515 protein binding
GO:0008158 hedgehog receptor activity
GO:0008201 heparin binding
GO:0015485 cholesterol binding
GO:0030332 cyclin binding
GO:0044877 protein-containing complex binding
GO:0097108 hedgehog family protein binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001658 branching involved in ureteric bud morphogenesis
GO:0001701 in utero embryonic development
GO:0001709 cell fate determination
GO:0001841 neural tube formation
GO:0001843 neural tube closure
GO:0003007 heart morphogenesis
GO:0007165 signal transduction
GO:0007224 smoothened signaling pathway
GO:0007286 spermatid development
GO:0007346 regulation of mitotic cell cycle
GO:0007389 pattern specification process
GO:0007420 brain development
GO:0008285 negative regulation of cell population proliferation
GO:0008544 epidermis development
GO:0008589 regulation of smoothened signaling pathway
GO:0009410 response to xenobiotic stimulus
GO:0009612 response to mechanical stimulus
GO:0009887 animal organ morphogenesis
GO:0009953 dorsal/ventral pattern formation
GO:0009957 epidermal cell fate specification
GO:0010157 response to chlorate
GO:0010839 negative regulation of keratinocyte proliferation
GO:0010875 positive regulation of cholesterol efflux
GO:0014070 response to organic cyclic compound
GO:0016485 protein processing
GO:0021522 spinal cord motor neuron differentiation
GO:0021532 neural tube patterning
GO:0021904 dorsal/ventral neural tube patterning
GO:0021997 neural plate axis specification
GO:0030326 embryonic limb morphogenesis
GO:0030850 prostate gland development
GO:0030879 mammary gland development
GO:0032355 response to estradiol
GO:0032526 response to retinoic acid
GO:0032880 regulation of protein localization
GO:0035108 limb morphogenesis
GO:0035137 hindlimb morphogenesis
GO:0040008 regulation of growth
GO:0040015 negative regulation of multicellular organism growth
GO:0042127 regulation of cell population proliferation
GO:0042593 glucose homeostasis
GO:0043433 negative regulation of DNA-binding transcription factor activity
GO:0043616 keratinocyte proliferation
GO:0045606 positive regulation of epidermal cell differentiation
GO:0045668 negative regulation of osteoblast differentiation
GO:0045879 negative regulation of smoothened signaling pathway
GO:0045892 negative regulation of DNA-templated transcription
GO:0045893 positive regulation of DNA-templated transcription
GO:0048568 embryonic organ development
GO:0048745 smooth muscle tissue development
GO:0050673 epithelial cell proliferation
GO:0050680 negative regulation of epithelial cell proliferation
GO:0051782 negative regulation of cell division
GO:0060037 pharyngeal system development
GO:0060603 mammary gland duct morphogenesis
GO:0060644 mammary gland epithelial cell differentiation
GO:0061005 cell differentiation involved in kidney development
GO:0061053 somite development
GO:0071397 cellular response to cholesterol
GO:0071679 commissural neuron axon guidance
GO:0072089 stem cell proliferation
GO:0072203 cell proliferation involved in metanephros development
GO:0072205 metanephric collecting duct development
GO:0072659 protein localization to plasma membrane
GO:0097421 liver regeneration
GO:2000647 negative regulation of stem cell proliferation
Cellular Component
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0005901 caveola
GO:0005929 cilium
GO:0016020 membrane
GO:0030496 midbody
GO:0030666 endocytic vesicle membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0044294 dendritic growth cone
GO:0044295 axonal growth cone
GO:0045177 apical part of cell
GO:0045211 postsynaptic membrane
GO:0048471 perinuclear region of cytoplasm
GO:0060170 ciliary membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6dmb, PDBe:6dmb, PDBj:6dmb
PDBsum6dmb
PubMed29954986
UniProtQ13635|PTC1_HUMAN Protein patched homolog 1 (Gene Name=PTCH1)

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