Structure

Physi-Chem Properties

Molecular Weight:  252.17
Volume:  260.141
LogP:  3.99
LogD:  3.367
LogS:  -4.487
# Rotatable Bonds:  0
TPSA:  37.59
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.622
Synthetic Accessibility Score:  5.156
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.677
MDCK Permeability:  2.6871754016610794e-05
Pgp-inhibitor:  0.996
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.145
Plasma Protein Binding (PPB):  69.17623138427734%
Volume Distribution (VD):  1.772
Pgp-substrate:  26.466148376464844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.739
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.902
CYP2C9-inhibitor:  0.061
CYP2C9-substrate:  0.027
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.466
CYP3A4-inhibitor:  0.092
CYP3A4-substrate:  0.372

ADMET: Excretion

Clearance (CL):  12.236
Half-life (T1/2):  0.28

ADMET: Toxicity

hERG Blockers:  0.116
Human Hepatotoxicity (H-HT):  0.23
Drug-inuced Liver Injury (DILI):  0.368
AMES Toxicity:  0.057
Rat Oral Acute Toxicity:  0.503
Maximum Recommended Daily Dose:  0.738
Skin Sensitization:  0.879
Carcinogencity:  0.537
Eye Corrosion:  0.972
Eye Irritation:  0.913
Respiratory Toxicity:  0.98

Download Data

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

  Natural Product: NPC474331

Natural Product ID:  NPC474331
Common Name*:   DKHWLZDWNCVYPO-SYPGZIFDSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DKHWLZDWNCVYPO-SYPGZIFDSA-N
Standard InCHI:  InChI=1S/C15H24O3/c1-13(2)8-11-14(3,18-11)6-5-10-15(4,17-10)7-9-12(13)16-9/h9-12H,5-8H2,1-4H3/t9-,10+,11-,12+,14-,15+/m0/s1
SMILES:  CC1(CC2C(O2)(CCC3C(O3)(CC4C1O4)C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL465351
PubChem CID:   44566709
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000159] Epoxides

*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 IC50 = 95000.0 nM PMID[559008]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 51.1 % PMID[559008]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 25.7 % PMID[559008]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 9.7 % PMID[559008]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 6.9 % PMID[559008]

☑ 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 NPC474331 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
0.8 Intermediate Similarity NPC170780
0.7692 Intermediate Similarity NPC224987
0.7627 Intermediate Similarity NPC172622
0.7097 Intermediate Similarity NPC199937
0.6825 Remote Similarity NPC476702
0.6774 Remote Similarity NPC475807
0.6719 Remote Similarity NPC165069
0.6613 Remote Similarity NPC475412
0.661 Remote Similarity NPC300189
0.6552 Remote Similarity NPC161473
0.6406 Remote Similarity NPC50435
0.6393 Remote Similarity NPC7491
0.6393 Remote Similarity NPC13789
0.6393 Remote Similarity NPC65786
0.6393 Remote Similarity NPC27853
0.6393 Remote Similarity NPC101285
0.6338 Remote Similarity NPC472952
0.6338 Remote Similarity NPC472950
0.6301 Remote Similarity NPC471769
0.625 Remote Similarity NPC253204
0.6216 Remote Similarity NPC469608
0.6207 Remote Similarity NPC307022
0.6164 Remote Similarity NPC108014
0.6164 Remote Similarity NPC476233
0.6129 Remote Similarity NPC119425
0.6129 Remote Similarity NPC291147
0.6129 Remote Similarity NPC322148
0.6081 Remote Similarity NPC470014
0.6081 Remote Similarity NPC23187
0.6066 Remote Similarity NPC471269
0.6066 Remote Similarity NPC45387
0.6032 Remote Similarity NPC476209
0.6029 Remote Similarity NPC33583
0.6029 Remote Similarity NPC161612
0.6027 Remote Similarity NPC268111
0.6 Remote Similarity NPC165755
0.6 Remote Similarity NPC240994
0.5972 Remote Similarity NPC470151
0.597 Remote Similarity NPC250836
0.5968 Remote Similarity NPC210316
0.5965 Remote Similarity NPC13105
0.5946 Remote Similarity NPC143250
0.5946 Remote Similarity NPC186109
0.5946 Remote Similarity NPC188793
0.5938 Remote Similarity NPC475968
0.5932 Remote Similarity NPC291724
0.5932 Remote Similarity NPC274261
0.5921 Remote Similarity NPC472951
0.5921 Remote Similarity NPC117137
0.5921 Remote Similarity NPC186588
0.5921 Remote Similarity NPC16449
0.5921 Remote Similarity NPC472943
0.5921 Remote Similarity NPC66766
0.5918 Remote Similarity NPC139569
0.5915 Remote Similarity NPC96322
0.5893 Remote Similarity NPC108441
0.5893 Remote Similarity NPC77550
0.589 Remote Similarity NPC93213
0.5882 Remote Similarity NPC469328
0.5875 Remote Similarity NPC137253
0.5857 Remote Similarity NPC304690
0.5857 Remote Similarity NPC74722
0.5846 Remote Similarity NPC204173
0.5844 Remote Similarity NPC473257
0.5833 Remote Similarity NPC476709
0.5821 Remote Similarity NPC140233
0.5821 Remote Similarity NPC287744
0.5818 Remote Similarity NPC302939
0.5818 Remote Similarity NPC287331
0.5806 Remote Similarity NPC223604
0.5797 Remote Similarity NPC259299
0.5797 Remote Similarity NPC179823
0.5789 Remote Similarity NPC80999
0.5781 Remote Similarity NPC215671
0.5781 Remote Similarity NPC87296
0.5781 Remote Similarity NPC475515
0.5781 Remote Similarity NPC182903
0.5775 Remote Similarity NPC471879
0.5758 Remote Similarity NPC185547
0.5758 Remote Similarity NPC95804
0.5753 Remote Similarity NPC308489
0.5753 Remote Similarity NPC475458
0.5753 Remote Similarity NPC190859
0.5738 Remote Similarity NPC36002
0.5738 Remote Similarity NPC102336
0.5735 Remote Similarity NPC476330
0.5735 Remote Similarity NPC215987
0.5735 Remote Similarity NPC61503
0.5735 Remote Similarity NPC306805
0.5733 Remote Similarity NPC471454
0.5714 Remote Similarity NPC305698
0.5696 Remote Similarity NPC260852
0.5694 Remote Similarity NPC470173
0.5694 Remote Similarity NPC1340
0.5694 Remote Similarity NPC195530
0.5694 Remote Similarity NPC187471
0.5694 Remote Similarity NPC252182
0.5694 Remote Similarity NPC470071
0.5692 Remote Similarity NPC185116
0.5692 Remote Similarity NPC9880
0.5692 Remote Similarity NPC87828
0.5692 Remote Similarity NPC230070
0.5686 Remote Similarity NPC328441
0.5676 Remote Similarity NPC186851
0.5667 Remote Similarity NPC314084
0.5658 Remote Similarity NPC475725
0.5658 Remote Similarity NPC177343
0.5658 Remote Similarity NPC272841
0.5658 Remote Similarity NPC477089
0.5641 Remote Similarity NPC216941
0.5636 Remote Similarity NPC82843
0.5634 Remote Similarity NPC269841
0.5634 Remote Similarity NPC329989
0.5634 Remote Similarity NPC470833
0.5634 Remote Similarity NPC253123
0.5634 Remote Similarity NPC239373
0.5625 Remote Similarity NPC86238
0.5625 Remote Similarity NPC475689
0.5625 Remote Similarity NPC470238
0.5625 Remote Similarity NPC236588
0.5625 Remote Similarity NPC138647
0.5616 Remote Similarity NPC123122
0.5616 Remote Similarity NPC476718
0.5616 Remote Similarity NPC470660
0.5616 Remote Similarity NPC474123
0.5616 Remote Similarity NPC143576
0.5616 Remote Similarity NPC470659
0.5606 Remote Similarity NPC472021
0.5606 Remote Similarity NPC66145
0.56 Remote Similarity NPC107963
0.56 Remote Similarity NPC170148

  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 NPC474331 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
0.6154 Remote Similarity NPD1460 Approved
0.6061 Remote Similarity NPD371 Approved
0.5926 Remote Similarity NPD1462 Approved
0.5893 Remote Similarity NPD386 Approved
0.5893 Remote Similarity NPD388 Approved
0.5818 Remote Similarity NPD367 Approved
0.5636 Remote Similarity NPD8958 Phase 2

  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