Structure

Physi-Chem Properties

Molecular Weight:  254.19
Volume:  268.698
LogP:  2.278
LogD:  2.163
LogS:  -3.272
# Rotatable Bonds:  1
TPSA:  49.69
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.753
Synthetic Accessibility Score:  5.213
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.744
MDCK Permeability:  2.7423040592111647e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.015

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.378
Plasma Protein Binding (PPB):  85.6851577758789%
Volume Distribution (VD):  1.325
Pgp-substrate:  15.345318794250488%

ADMET: Metabolism

CYP1A2-inhibitor:  0.036
CYP1A2-substrate:  0.299
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.85
CYP2C9-inhibitor:  0.07
CYP2C9-substrate:  0.317
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.682
CYP3A4-inhibitor:  0.062
CYP3A4-substrate:  0.219

ADMET: Excretion

Clearance (CL):  8.02
Half-life (T1/2):  0.602

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.313
Drug-inuced Liver Injury (DILI):  0.035
AMES Toxicity:  0.033
Rat Oral Acute Toxicity:  0.076
Maximum Recommended Daily Dose:  0.507
Skin Sensitization:  0.491
Carcinogencity:  0.055
Eye Corrosion:  0.128
Eye Irritation:  0.873
Respiratory Toxicity:  0.684

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC475412

Natural Product ID:  NPC475412
Common Name*:   HDEDHTVUKLACPT-CMUJWSKESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HDEDHTVUKLACPT-CMUJWSKESA-N
Standard InCHI:  InChI=1S/C15H26O3/c1-13(2)8-11-10(13)4-6-14(3)12(17)5-7-15(11,9-16)18-14/h10-12,16-17H,4-9H2,1-3H3/t10-,11?,12-,14-,15+/m1/s1
SMILES:  OC[C@]12CC[C@H]([C@@](O1)(C)CC[C@@H]1C2CC1(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL505090
PubChem CID:   44566706
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001729] Oxepanes

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO7630 Cyperus longus Species Cyperaceae Eukaryota n.a. Egyptian herbal medicine n.a. PMID[15104485]
NPO7630 Cyperus longus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 45.9 % PMID[571050]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 19.9 % PMID[571050]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 10.4 % PMID[571050]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 5.7 % PMID[571050]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC475412 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9153 High Similarity NPC475807
0.7969 Intermediate Similarity NPC199937
0.7619 Intermediate Similarity NPC185116
0.75 Intermediate Similarity NPC161473
0.746 Intermediate Similarity NPC475515
0.746 Intermediate Similarity NPC215671
0.746 Intermediate Similarity NPC87296
0.7385 Intermediate Similarity NPC172622
0.7344 Intermediate Similarity NPC475968
0.7313 Intermediate Similarity NPC165069
0.7164 Intermediate Similarity NPC476702
0.7162 Intermediate Similarity NPC188793
0.7101 Intermediate Similarity NPC33583
0.7101 Intermediate Similarity NPC161612
0.6986 Remote Similarity NPC308489
0.6986 Remote Similarity NPC470151
0.6984 Remote Similarity NPC471269
0.6892 Remote Similarity NPC472952
0.6892 Remote Similarity NPC472950
0.6857 Remote Similarity NPC179823
0.6849 Remote Similarity NPC143576
0.6849 Remote Similarity NPC470660
0.6849 Remote Similarity NPC470659
0.6842 Remote Similarity NPC177343
0.6842 Remote Similarity NPC272841
0.6833 Remote Similarity NPC294858
0.6825 Remote Similarity NPC53209
0.6806 Remote Similarity NPC471879
0.6795 Remote Similarity NPC473257
0.6795 Remote Similarity NPC216941
0.6769 Remote Similarity NPC322148
0.6769 Remote Similarity NPC119425
0.6757 Remote Similarity NPC470630
0.6757 Remote Similarity NPC200167
0.6757 Remote Similarity NPC53868
0.6757 Remote Similarity NPC209666
0.6757 Remote Similarity NPC166250
0.6757 Remote Similarity NPC31046
0.6753 Remote Similarity NPC170595
0.6712 Remote Similarity NPC157777
0.6712 Remote Similarity NPC131506
0.6711 Remote Similarity NPC64081
0.6711 Remote Similarity NPC474574
0.6709 Remote Similarity NPC475849
0.6667 Remote Similarity NPC91387
0.6667 Remote Similarity NPC270306
0.6667 Remote Similarity NPC253123
0.6667 Remote Similarity NPC94897
0.6667 Remote Similarity NPC231680
0.6667 Remote Similarity NPC470833
0.6625 Remote Similarity NPC470070
0.6625 Remote Similarity NPC474266
0.662 Remote Similarity NPC477760
0.662 Remote Similarity NPC477754
0.662 Remote Similarity NPC477761
0.662 Remote Similarity NPC477759
0.662 Remote Similarity NPC477758
0.6613 Remote Similarity NPC474331
0.6613 Remote Similarity NPC307022
0.661 Remote Similarity NPC108441
0.661 Remote Similarity NPC77550
0.6585 Remote Similarity NPC268633
0.6585 Remote Similarity NPC107603
0.6579 Remote Similarity NPC279575
0.6571 Remote Similarity NPC471200
0.6571 Remote Similarity NPC472946
0.6571 Remote Similarity NPC250836
0.6552 Remote Similarity NPC144891
0.6538 Remote Similarity NPC477282
0.6538 Remote Similarity NPC81074
0.6533 Remote Similarity NPC472945
0.6533 Remote Similarity NPC472944
0.6533 Remote Similarity NPC138273
0.6522 Remote Similarity NPC50435
0.6515 Remote Similarity NPC291147
0.6515 Remote Similarity NPC236588
0.65 Remote Similarity NPC198540
0.65 Remote Similarity NPC287550
0.65 Remote Similarity NPC176309
0.65 Remote Similarity NPC147343
0.65 Remote Similarity NPC223468
0.65 Remote Similarity NPC84030
0.6494 Remote Similarity NPC11907
0.6494 Remote Similarity NPC133596
0.6494 Remote Similarity NPC476719
0.6486 Remote Similarity NPC470173
0.6486 Remote Similarity NPC8004
0.6486 Remote Similarity NPC127283
0.6479 Remote Similarity NPC477752
0.6479 Remote Similarity NPC477751
0.6479 Remote Similarity NPC477756
0.6479 Remote Similarity NPC477764
0.6463 Remote Similarity NPC290731
0.6462 Remote Similarity NPC45387
0.6462 Remote Similarity NPC300189
0.6456 Remote Similarity NPC16449
0.6456 Remote Similarity NPC186588
0.6456 Remote Similarity NPC472951
0.6456 Remote Similarity NPC117137
0.6456 Remote Similarity NPC472943
0.6456 Remote Similarity NPC66766
0.6447 Remote Similarity NPC139765
0.6447 Remote Similarity NPC131584
0.642 Remote Similarity NPC241959
0.6418 Remote Similarity NPC476209
0.6418 Remote Similarity NPC47663
0.641 Remote Similarity NPC477089
0.6406 Remote Similarity NPC36002
0.6406 Remote Similarity NPC102336
0.64 Remote Similarity NPC476709
0.64 Remote Similarity NPC248427
0.64 Remote Similarity NPC83368
0.64 Remote Similarity NPC95165
0.6386 Remote Similarity NPC476217
0.6386 Remote Similarity NPC472745
0.6375 Remote Similarity NPC470156
0.6364 Remote Similarity NPC136424
0.6364 Remote Similarity NPC293223
0.6364 Remote Similarity NPC107963
0.6364 Remote Similarity NPC329626
0.6364 Remote Similarity NPC170780
0.6351 Remote Similarity NPC282454
0.6341 Remote Similarity NPC166279
0.6341 Remote Similarity NPC474156
0.6338 Remote Similarity NPC260116
0.6316 Remote Similarity NPC190859
0.6316 Remote Similarity NPC228994
0.6316 Remote Similarity NPC10476
0.6316 Remote Similarity NPC192501
0.631 Remote Similarity NPC189777
0.631 Remote Similarity NPC233744
0.6296 Remote Similarity NPC475388
0.6296 Remote Similarity NPC477446
0.6296 Remote Similarity NPC470155
0.6296 Remote Similarity NPC477447
0.6296 Remote Similarity NPC102156
0.6296 Remote Similarity NPC148740
0.6286 Remote Similarity NPC209686
0.6286 Remote Similarity NPC249078
0.6286 Remote Similarity NPC235788
0.6286 Remote Similarity NPC236099
0.6282 Remote Similarity NPC214030
0.6282 Remote Similarity NPC83108
0.6269 Remote Similarity NPC135438
0.6267 Remote Similarity NPC109457
0.6267 Remote Similarity NPC470071
0.6267 Remote Similarity NPC1340
0.6267 Remote Similarity NPC252182
0.6267 Remote Similarity NPC157422
0.6267 Remote Similarity NPC187471
0.6267 Remote Similarity NPC100586
0.6265 Remote Similarity NPC290612
0.625 Remote Similarity NPC473899
0.625 Remote Similarity NPC244869
0.625 Remote Similarity NPC300235
0.625 Remote Similarity NPC476136
0.625 Remote Similarity NPC476149
0.6234 Remote Similarity NPC317242
0.6234 Remote Similarity NPC196136
0.6234 Remote Similarity NPC36479
0.6234 Remote Similarity NPC243027
0.6234 Remote Similarity NPC150938
0.6234 Remote Similarity NPC158208
0.622 Remote Similarity NPC29342
0.622 Remote Similarity NPC477285
0.622 Remote Similarity NPC269684
0.622 Remote Similarity NPC111582
0.622 Remote Similarity NPC2572
0.6216 Remote Similarity NPC66407
0.6203 Remote Similarity NPC252483
0.6203 Remote Similarity NPC191345
0.6203 Remote Similarity NPC43463
0.6203 Remote Similarity NPC475980
0.619 Remote Similarity NPC471410
0.619 Remote Similarity NPC471411
0.6184 Remote Similarity NPC473238
0.6184 Remote Similarity NPC470610
0.6184 Remote Similarity NPC472341
0.6184 Remote Similarity NPC123122
0.6184 Remote Similarity NPC153719
0.6176 Remote Similarity NPC182903
0.6173 Remote Similarity NPC470154
0.6167 Remote Similarity NPC240994
0.6164 Remote Similarity NPC253303
0.6164 Remote Similarity NPC269077
0.6164 Remote Similarity NPC476928
0.6164 Remote Similarity NPC286842
0.6163 Remote Similarity NPC97103
0.6163 Remote Similarity NPC115607
0.6154 Remote Similarity NPC163597
0.6154 Remote Similarity NPC470145
0.6154 Remote Similarity NPC470766
0.6154 Remote Similarity NPC470176
0.6154 Remote Similarity NPC170148
0.6145 Remote Similarity NPC18953
0.6143 Remote Similarity NPC95804
0.6143 Remote Similarity NPC185547
0.6133 Remote Similarity NPC51956
0.6133 Remote Similarity NPC29005
0.6133 Remote Similarity NPC5209

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC475412 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.7692 Intermediate Similarity NPD371 Approved
0.6757 Remote Similarity NPD1810 Approved
0.6757 Remote Similarity NPD1811 Approved
0.661 Remote Similarity NPD386 Approved
0.661 Remote Similarity NPD388 Approved
0.65 Remote Similarity NPD384 Approved
0.65 Remote Similarity NPD385 Approved
0.6133 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6133 Remote Similarity NPD2686 Approved
0.6133 Remote Similarity NPD2254 Approved
0.6133 Remote Similarity NPD2687 Approved
0.6 Remote Similarity NPD367 Approved
0.6 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5854 Remote Similarity NPD6928 Phase 2
0.5833 Remote Similarity NPD3670 Clinical (unspecified phase)
0.5833 Remote Similarity NPD3669 Approved
0.5747 Remote Similarity NPD7524 Approved
0.5606 Remote Similarity NPD905 Approved
0.5606 Remote Similarity NPD904 Phase 3
0.5604 Remote Similarity NPD8171 Discontinued

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data