Structure of PDB 6rvd Chain B Binding Site BS01

Receptor Information
>6rvd Chain B (length=978) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLWLRAKFQRLLFKLGCYIQKNCGKFLVVGLLIFGAFAVGLKAANLETNV
EELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMIQTPKEEGANVLTTEAL
LQHLDSALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQIIEYLYP
CLIITPLDCFWEGAKLQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQV
DSWEEMLNKAEVGHGYMDRPCLNPADPDCPATAPNKNSTKPLDMALVLNG
GCHGLSRKYMHWQEELIVGGTVKNSTGKLVSAHALQTMFQLMTPKQMYEH
FKGYEYVSHINWNEDKAAAILEAWQRTYVEVVHQSVAQNSTQKVLSFTTT
TLDDILKSFSDVSVIRVASGYLLMLAYACLTMLRWDCSKSQGAVGLAGVL
LVALSVAAGLGLCSLIGISFNAATTQVLPFLALGVGVDDVFLLAHAFSET
GQNKRIPFEDRTGECLKRTGASVALTSISNVTAFFMAALIPIPALRAFSL
QAAVVVVFNFAMVLLIFPAILSMDLYRREDSSFAEKHYAPFLLKPKAKVV
VIFLFLGLLGVSLYGTTRVRDGLDLTDIVPRETREYDFIAAQFKYFSFYN
MYIVTQKADYPNIQHLLYDLHRSFSNVKYVMLEENKQLPKMWLHYFRDWL
QGLQDAFDSDWETGKIMPNNYKNGSDDGVLAYKLLVQTGSRDKPIDISQL
TKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQANIRPHRPEWVHDK
ADYMPETRLRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICSNYT
SLGLSSYPNGYPFLFWEQYIGLRHWLLLFISVVLACTFLVCAVFLLNPWT
AGIIVMVLALMTVELFGMMGLIGIKLSAVPVVILIASVGIGVEFTVHVAL
AFLTAIGDKNRRAVLALEHMFAPVLDGAVSTLLGVLMLAGSEFDFIVRYF
FAVLAILTILGVLNGLVLLPVLLSFFGP
Ligand information
Ligand IDCLR
InChIInChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
InChIKeyHVYWMOMLDIMFJA-DPAQBDIFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C
CACTVS 3.341CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
ACDLabs 10.04OC4CCC3(C(=CCC2C1C(C(C(C)CCCC(C)C)CC1)(C)CCC23)C4)C
OpenEye OEToolkits 1.5.0CC(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)O)C)C
CACTVS 3.341CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](O)CC[C]4(C)[CH]3CC[C]12C
FormulaC27 H46 O
NameCHOLESTEROL
ChEMBLCHEMBL112570
DrugBankDB04540
ZINCZINC000003875383
PDB chain6rvd Chain B Residue 1501 [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]
PDB6rvd The morphogen Sonic hedgehog inhibits its receptor Patched by a pincer grasp mechanism.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		M216 Y224 P225 L282 A285 S331 Y334 M335 V932 A936
Binding residue
(residue number reindexed from 1)		M141 Y149 P150 L207 A210 S256 Y259 M260 V730 A734
Annotation score4
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6rvd, PDBe:6rvd, PDBj:6rvd
PDBsum6rvd
PubMed31548691
UniProtQ13635|PTC1_HUMAN Protein patched homolog 1 (Gene Name=PTCH1)

[Back to BioLiP]