Structure

Physi-Chem Properties

Molecular Weight:  356.13
Volume:  360.456
LogP:  4.256
LogD:  2.763
LogS:  -3.368
# Rotatable Bonds:  3
TPSA:  107.22
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.493
Synthetic Accessibility Score:  3.32
Fsp3:  0.25
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.131
MDCK Permeability:  8.879023880581371e-06
Pgp-inhibitor:  0.026
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.975
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.005
Plasma Protein Binding (PPB):  98.43241882324219%
Volume Distribution (VD):  0.588
Pgp-substrate:  2.9242637157440186%

ADMET: Metabolism

CYP1A2-inhibitor:  0.641
CYP1A2-substrate:  0.345
CYP2C19-inhibitor:  0.788
CYP2C19-substrate:  0.057
CYP2C9-inhibitor:  0.876
CYP2C9-substrate:  0.787
CYP2D6-inhibitor:  0.754
CYP2D6-substrate:  0.312
CYP3A4-inhibitor:  0.216
CYP3A4-substrate:  0.142

ADMET: Excretion

Clearance (CL):  18.692
Half-life (T1/2):  0.771

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.815
Drug-inuced Liver Injury (DILI):  0.914
AMES Toxicity:  0.132
Rat Oral Acute Toxicity:  0.757
Maximum Recommended Daily Dose:  0.736
Skin Sensitization:  0.943
Carcinogencity:  0.267
Eye Corrosion:  0.003
Eye Irritation:  0.903
Respiratory Toxicity:  0.612

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  Natural Product: NPC34550

Natural Product ID:  NPC34550
Common Name*:   WTHUMSLQUHCWCH-CMKODMSKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WTHUMSLQUHCWCH-CMKODMSKSA-N
Standard InCHI:  InChI=1S/C20H30O/c1-13(2)14-6-8-16-15(12-14)7-9-17-19(3,4)18(21)10-11-20(16,17)5/h6,8,12-13,17-18,21H,7,9-11H2,1-5H3/t17-,18-,20+/m0/s1
SMILES:  CC(C)c1ccc2c(CC[C@H]3C(C)(C)[C@H](CC[C@]23C)O)c1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   13996029
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
NPO21373 Vitex trifolia Species Lamiaceae Eukaryota n.a. fruit n.a. PMID[15577254]
NPO21373 Vitex trifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[15621610]
NPO17785 Avrainvillea nigricans Species Udoteaceae Eukaryota n.a. n.a. n.a. PMID[16180830]
NPO22123 Disepalum plagioneurum Species Annonaceae Eukaryota leaves Tam Kim, Cao Bang Province, in North Vietnam 2000-JUN PMID[16989521]
NPO20954 Haloxylon salicornicum Species Chenopodiaceae Eukaryota whole plant Cholistan desert near district Bahawalpur (Punjab), Pakistan 2003-Oct PMID[20542692]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[2082684]
NPO18212 Rhododendron ferrugineum Species Ericaceae Eukaryota n.a. leaf n.a. PMID[21443171]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[21922656]
NPO21373 Vitex trifolia Species Lamiaceae Eukaryota fruits n.a. n.a. PMID[23327905]
NPO18530 Shigella flexneri Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26918643]
NPO21373 Vitex trifolia Species Lamiaceae Eukaryota Leaves n.a. n.a. PMID[28453270]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[3254039]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[3256207]
NPO17785 Avrainvillea nigricans Species Udoteaceae Eukaryota n.a. n.a. n.a. PMID[3668556]
NPO23178 Jasminum grandiflorum Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22188 Piper aequale Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23135 Formica fusca Species Formicidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22819 Rodgersia podophylla Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21373 Vitex trifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21373 Vitex trifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23135 Formica fusca Species Formicidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23178 Jasminum grandiflorum Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20954 Haloxylon salicornicum Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21875 Persea indica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22819 Rodgersia podophylla Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22188 Piper aequale Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23135 Formica fusca Species Formicidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21373 Vitex trifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21373 Vitex trifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21247 Nephroma australe Species Nephromataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20954 Haloxylon salicornicum Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18212 Rhododendron ferrugineum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22819 Rodgersia podophylla Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21998 Corydalis cornuta Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23178 Jasminum grandiflorum Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20043 Vallaris solanacea Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22940 Delphinium campylocentrum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20360 Mentha pulegiformis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18530 Shigella flexneri Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22454 Picris radicata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21373 Vitex trifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23135 Formica fusca Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18571 Drypetes roxburghii Species Putranjivaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20678 Grindelia nana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21298 Leucanthemum maximum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21505 Calea megacephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19074 Buddleja variabilis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20184 Streptomyces misawanensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO20808 Halopitys incurvus n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO22062 Leptothorax acervorum Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16146 Osmundaria colensoi Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21636 Didemnum inarmatum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20536 Salvia nubicola Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22582 Smenospongia echina Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21798 Dacrydium biforme Species Mytilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17108 Lecanora lividocinerea Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7865 Scapania nemorea Species Scapaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22762 Eremophila serrulata Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21736 Abies nobilis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21875 Persea indica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22123 Disepalum plagioneurum Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22248 Alkanna hirsutissima Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14394 Hakea saligna Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22994 Cordyline indivisa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5952 Phegopteris bukoensis Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22323 Pinus picea Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22710 Acrocomia sclerocarpa Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14247 Melaleuca uncinata Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12225 Amsinckia menziesii Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22188 Piper aequale Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23057 Primula hirsuta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19921 Polyphaga sinensis Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7080 Monascus purpureus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21113 Coronophora gregaria Species Nitschkiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17785 Avrainvillea nigricans Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19694 Senecio scandens Species Asteraceae 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 NPC34550 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 NPC34550 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