Structure

Physi-Chem Properties

Molecular Weight:  300.21
Volume:  335.841
LogP:  5.278
LogD:  4.469
LogS:  -5.545
# Rotatable Bonds:  1
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.775
Synthetic Accessibility Score:  3.536
Fsp3:  0.65
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.872
MDCK Permeability:  1.60232466441812e-05
Pgp-inhibitor:  0.903
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.978
30% Bioavailability (F30%):  0.973

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.257
Plasma Protein Binding (PPB):  97.18192291259766%
Volume Distribution (VD):  1.17
Pgp-substrate:  4.3170671463012695%

ADMET: Metabolism

CYP1A2-inhibitor:  0.339
CYP1A2-substrate:  0.826
CYP2C19-inhibitor:  0.684
CYP2C19-substrate:  0.864
CYP2C9-inhibitor:  0.488
CYP2C9-substrate:  0.905
CYP2D6-inhibitor:  0.597
CYP2D6-substrate:  0.645
CYP3A4-inhibitor:  0.542
CYP3A4-substrate:  0.444

ADMET: Excretion

Clearance (CL):  9.47
Half-life (T1/2):  0.092

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.105
Drug-inuced Liver Injury (DILI):  0.352
AMES Toxicity:  0.038
Rat Oral Acute Toxicity:  0.412
Maximum Recommended Daily Dose:  0.911
Skin Sensitization:  0.526
Carcinogencity:  0.082
Eye Corrosion:  0.011
Eye Irritation:  0.908
Respiratory Toxicity:  0.938

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC265784

Natural Product ID:  NPC265784
Common Name*:   IPEHJNRNYPOFII-ROPPNANJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  IPEHJNRNYPOFII-ROPPNANJSA-N
Standard InCHI:  InChI=1S/C20H28O2/c1-12(2)13-9-14-15(10-16(13)21)20(5)8-6-7-19(3,4)18(20)11-17(14)22/h9-10,12,18,21H,6-8,11H2,1-5H3/t18?,20-/m1/s1
SMILES:  CC(C)c1cc2c(cc1O)[C@@]1(C)CCCC(C)(C)C1CC2=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5321549
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO18562 Cephalotaxus wilsoniana Species Taxaceae Eukaryota n.a. stem n.a. PMID[10726874]
NPO18562 Cephalotaxus wilsoniana Species Taxaceae Eukaryota n.a. twig n.a. PMID[10726874]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. PMID[11339628]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[11374966]
NPO18562 Cephalotaxus wilsoniana Species Taxaceae Eukaryota n.a. twig n.a. PMID[12499600]
NPO18562 Cephalotaxus wilsoniana Species Taxaceae Eukaryota n.a. stem n.a. PMID[12499600]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16038550]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[17217287]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. bark n.a. PMID[17260795]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17583950]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18855446]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. Daejeon, Korea 2007-Jan PMID[19670875]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20455578]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20515057]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. seed n.a. PMID[20822014]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21775156]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. root n.a. PMID[22547314]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23286284]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24108414]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota root bark Bozhou, Anhui Province, China 2010-AUG PMID[24377852]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. flower n.a. PMID[24504864]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota Flowers LuoYang, HeNan, China n.a. PMID[24621197]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[24913660]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27569393]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29185738]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30351923]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[3655791]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota roots n.a. n.a. PMID[9834151]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28301 Clerodendron cyrtophyllum n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17259 Thuja standishii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29741 Paeonia moutan Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18562 Cephalotaxus wilsoniana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18562 Cephalotaxus wilsoniana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28301 Clerodendron cyrtophyllum n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17259 Thuja standishii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30139 Salvia przewalskll Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29741 Paeonia moutan Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17259 Thuja standishii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18562 Cephalotaxus wilsoniana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22550 Paeonia suffruticosa Species Paeoniaceae 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

☑ 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 NPC265784 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

  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 NPC265784 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

  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