Structure

Physi-Chem Properties

Molecular Weight:  274.2
Volume:  293.873
LogP:  2.588
LogD:  2.735
LogS:  -2.326
# Rotatable Bonds:  0
TPSA:  32.67
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.68
Synthetic Accessibility Score:  5.508
Fsp3:  0.882
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:  -4.869
MDCK Permeability:  1.1374180758139119e-05
Pgp-inhibitor:  0.054
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.437
30% Bioavailability (F30%):  0.928

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.967
Plasma Protein Binding (PPB):  26.587154388427734%
Volume Distribution (VD):  1.392
Pgp-substrate:  71.69876098632812%

ADMET: Metabolism

CYP1A2-inhibitor:  0.039
CYP1A2-substrate:  0.43
CYP2C19-inhibitor:  0.069
CYP2C19-substrate:  0.938
CYP2C9-inhibitor:  0.038
CYP2C9-substrate:  0.296
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.644
CYP3A4-inhibitor:  0.191
CYP3A4-substrate:  0.692

ADMET: Excretion

Clearance (CL):  9.3
Half-life (T1/2):  0.75

ADMET: Toxicity

hERG Blockers:  0.051
Human Hepatotoxicity (H-HT):  0.475
Drug-inuced Liver Injury (DILI):  0.182
AMES Toxicity:  0.086
Rat Oral Acute Toxicity:  0.456
Maximum Recommended Daily Dose:  0.844
Skin Sensitization:  0.882
Carcinogencity:  0.717
Eye Corrosion:  0.004
Eye Irritation:  0.029
Respiratory Toxicity:  0.881

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Similar NPs/Drugs  

  Natural Product: NPC67342

Natural Product ID:  NPC67342
Common Name*:   HXJHQEWSHQXRPH-IPJQOSJUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HXJHQEWSHQXRPH-IPJQOSJUSA-N
Standard InCHI:  InChI=1S/C17H26N2O/c1-11-8-12-9-15-14(5-6-16(20)18-15)17(10-11)13(12)4-3-7-19(17)2/h11-13H,3-10H2,1-2H3,(H,18,20)/p+1/t11-,12+,13-,17-/m1/s1
SMILES:  C[C@@H]1C[C@H]2CC3=C(CCC(=[NH+]3)O)[C@@]3(C1)[C@@H]2CCCN3C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5462446
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. seed n.a. DOI[10.1016/S0031-9422(98)00552-4]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[12932142]
NPO19825 Litsea japonica Species Lauraceae Eukaryota leaves n.a. n.a. PMID[14575444]
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. Formosan soft coral n.a. PMID[16309317]
NPO24855 Callicarpa americana Species Lamiaceae Eukaryota fruiting branches n.a. n.a. PMID[17279798]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. PMID[19245240]
NPO7688 Artemisia selengensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29460 Petiveria alliacea Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29277 Lycopodium obscurum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29460 Petiveria alliacea Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24542 Doris obsoleta Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17577 Azalea ovata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26498 Vernonia cumingiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29460 Petiveria alliacea Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18499 Podium complanatum Species Sphecidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19565 Crocus chrysanthus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28418 Grateloupia filicina Species Halymeniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11060 Doris luteorosea Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19869 Fusicolla aquaeductuum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26775 Shorea wangtianshuea Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29521 Genista purgans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28055 Perymenium berlandieri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29277 Lycopodium obscurum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17887 Penstemon centranthifolius Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29087 Ligularia brachyphylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9799 Hebeloma longicaudum Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27361 Hylobius abietis Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29247 Wahlenbergia marginata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29261 Bryothamnion triquetrum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19234 Hymenopappus newberryi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27125 Hovea linearis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26989 Delphinium geyeri Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18518 Haematomma nemetzii Species Haematommataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19696 Othonna quercifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19298 Gerbera crocea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15450 Minuria leptophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27937 Centaurea iberica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18023 Vitex quinata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18357 Euphorbia sanctae-catharinae Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24832 Eriocaulon ligulatum Species Eriocaulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24978 Psila boliviensis Species Psilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19825 Litsea japonica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24855 Callicarpa americana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25798 Gunnera perpensa Species Gunneraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17341 Gambeya africana n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26339 Dillenia philippinensis Species Dilleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21360 Cordia corymbosa Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21044 Sphaerellopsis filum Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7688 Artemisia selengensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22646 Malouetia tamaquarina Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26662 Chrysanthemum foeniculaceum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29522 Cuscuta salina Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24225 Alexandrium peruvianum Species Gonyaulacaceae 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 NPC67342 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 NPC67342 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