Structure of PDB 5mkf Chain D Binding Site BS01

Receptor Information
>5mkf Chain D (length=481) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSK
TEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENL
LLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGT
AWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVW
LDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIR
YVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVI
VVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAV
TVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQL
AYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTF
VFFMFFILLNMFLAIINDTYSEVKSDLAQQK
Ligand information
Ligand IDCHS
InChIInChI=1S/C11H21NO3/c12-9(10(13)7-11(14)15)6-8-4-2-1-3-5-8/h8-10,13H,1-7,12H2,(H,14,15)/t9-,10-/m0/s1
InChIKeyUQWNNUPJBDWRHC-UWVGGRQHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1CCC(CC1)CC(C(CC(=O)O)O)N
CACTVS 3.341N[C@@H](CC1CCCCC1)[C@@H](O)CC(O)=O
ACDLabs 10.04O=C(O)CC(O)C(N)CC1CCCCC1
OpenEye OEToolkits 1.5.0C1CCC(CC1)C[C@@H]([C@H](CC(=O)O)O)N
CACTVS 3.341N[CH](CC1CCCCC1)[CH](O)CC(O)=O
FormulaC11 H21 N O3
Name4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID
ChEMBL
DrugBank
ZINCZINC000002526313
PDB chain5mkf Chain D Residue 1011 [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]
PDB5mkf Molecular insights into lipid-assisted Ca(2+) regulation of the TRP channel Polycystin-2.
Resolution4.2 Å
Binding residue
(original residue number in PDB)		L231 I232 C235
Binding residue
(residue number reindexed from 1)		L17 I18 C21
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005102 signaling receptor binding
GO:0005244 voltage-gated monoatomic ion channel activity
GO:0005245 voltage-gated calcium channel activity
GO:0005248 voltage-gated sodium channel activity
GO:0005249 voltage-gated potassium channel activity
GO:0005261 monoatomic cation channel activity
GO:0005262 calcium channel activity
GO:0005267 potassium channel activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008092 cytoskeletal protein binding
GO:0015267 channel activity
GO:0015271 outward rectifier potassium channel activity
GO:0022843 voltage-gated monoatomic cation channel activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0042805 actinin binding
GO:0043398 HLH domain binding
GO:0044325 transmembrane transporter binding
GO:0046872 metal ion binding
GO:0048763 calcium-induced calcium release activity
GO:0051117 ATPase binding
GO:0051219 phosphoprotein binding
GO:0051371 muscle alpha-actinin binding
GO:0051393 alpha-actinin binding
GO:0140416 transcription regulator inhibitor activity
Biological Process
GO:0001658 branching involved in ureteric bud morphogenesis
GO:0001822 kidney development
GO:0001889 liver development
GO:0001892 embryonic placenta development
GO:0001947 heart looping
GO:0003127 detection of nodal flow
GO:0006816 calcium ion transport
GO:0006874 intracellular calcium ion homeostasis
GO:0007166 cell surface receptor signaling pathway
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0007259 cell surface receptor signaling pathway via JAK-STAT
GO:0007368 determination of left/right symmetry
GO:0007507 heart development
GO:0008285 negative regulation of cell population proliferation
GO:0010628 positive regulation of gene expression
GO:0016055 Wnt signaling pathway
GO:0019722 calcium-mediated signaling
GO:0021510 spinal cord development
GO:0021915 neural tube development
GO:0031587 positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity
GO:0034614 cellular response to reactive oxygen species
GO:0035502 metanephric part of ureteric bud development
GO:0035725 sodium ion transmembrane transport
GO:0035904 aorta development
GO:0042127 regulation of cell population proliferation
GO:0044782 cilium organization
GO:0045429 positive regulation of nitric oxide biosynthetic process
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0050982 detection of mechanical stimulus
GO:0051209 release of sequestered calcium ion into cytosol
GO:0051262 protein tetramerization
GO:0051289 protein homotetramerization
GO:0051290 protein heterotetramerization
GO:0051298 centrosome duplication
GO:0051649 establishment of localization in cell
GO:0051726 regulation of cell cycle
GO:0060674 placenta blood vessel development
GO:0061333 renal tubule morphogenesis
GO:0061441 renal artery morphogenesis
GO:0070588 calcium ion transmembrane transport
GO:0071277 cellular response to calcium ion
GO:0071320 cellular response to cAMP
GO:0071464 cellular response to hydrostatic pressure
GO:0071470 cellular response to osmotic stress
GO:0071498 cellular response to fluid shear stress
GO:0071805 potassium ion transmembrane transport
GO:0071910 determination of liver left/right asymmetry
GO:0072075 metanephric mesenchyme development
GO:0072164 mesonephric tubule development
GO:0072177 mesonephric duct development
GO:0072208 metanephric smooth muscle tissue development
GO:0072214 metanephric cortex development
GO:0072218 metanephric ascending thin limb development
GO:0072219 metanephric cortical collecting duct development
GO:0072235 metanephric distal tubule development
GO:0072284 metanephric S-shaped body morphogenesis
GO:0090279 regulation of calcium ion import
GO:0098662 inorganic cation transmembrane transport
GO:2000134 negative regulation of G1/S transition of mitotic cell cycle
Cellular Component
GO:0002133 polycystin complex
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005929 cilium
GO:0009925 basal plasma membrane
GO:0016020 membrane
GO:0016323 basolateral plasma membrane
GO:0030027 lamellipodium
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031514 motile cilium
GO:0031982 vesicle
GO:0034702 monoatomic ion channel complex
GO:0034703 cation channel complex
GO:0036064 ciliary basal body
GO:0043226 organelle
GO:0045180 basal cortex
GO:0060170 ciliary membrane
GO:0070062 extracellular exosome
GO:0072686 mitotic spindle
GO:0097730 non-motile cilium
GO:0098553 lumenal side of endoplasmic reticulum membrane
GO:0098554 cytoplasmic side of endoplasmic reticulum membrane
GO:0140494 migrasome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5mkf, PDBe:5mkf, PDBj:5mkf
PDBsum5mkf
PubMed28092368
UniProtQ13563|PKD2_HUMAN Polycystin-2 (Gene Name=PKD2)

[Back to BioLiP]