Structure

Physi-Chem Properties

Molecular Weight:  242.18
Volume:  265.151
LogP:  2.705
LogD:  2.404
LogS:  -2.02
# Rotatable Bonds:  0
TPSA:  24.92
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.756
Synthetic Accessibility Score:  4.84
Fsp3:  0.688
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:  -4.739
MDCK Permeability:  1.5774101484566927e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.997
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.962
30% Bioavailability (F30%):  0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.951
Plasma Protein Binding (PPB):  24.650054931640625%
Volume Distribution (VD):  3.053
Pgp-substrate:  63.08420181274414%

ADMET: Metabolism

CYP1A2-inhibitor:  0.129
CYP1A2-substrate:  0.852
CYP2C19-inhibitor:  0.304
CYP2C19-substrate:  0.924
CYP2C9-inhibitor:  0.058
CYP2C9-substrate:  0.717
CYP2D6-inhibitor:  0.28
CYP2D6-substrate:  0.879
CYP3A4-inhibitor:  0.451
CYP3A4-substrate:  0.431

ADMET: Excretion

Clearance (CL):  6.396
Half-life (T1/2):  0.508

ADMET: Toxicity

hERG Blockers:  0.387
Human Hepatotoxicity (H-HT):  0.749
Drug-inuced Liver Injury (DILI):  0.058
AMES Toxicity:  0.189
Rat Oral Acute Toxicity:  0.825
Maximum Recommended Daily Dose:  0.887
Skin Sensitization:  0.947
Carcinogencity:  0.071
Eye Corrosion:  0.01
Eye Irritation:  0.035
Respiratory Toxicity:  0.969

Download Data

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

  Natural Product: NPC299954

Natural Product ID:  NPC299954
Common Name*:   JJPMUZRSJKMFRK-OQMKEHIESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JJPMUZRSJKMFRK-OQMKEHIESA-N
Standard InCHI:  InChI=1S/C16H22N2/c1-11-8-12-9-15-14(5-2-6-17-15)16(10-11)13(12)4-3-7-18-16/h2,5-6,11-13,18H,3-4,7-10H2,1H3/t11-,12+,13-,16-/m1/s1
SMILES:  C[C@@H]1C[C@H]2Cc3c(cccn3)[C@@]3(C1)[C@@H]2CCCN3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5462443
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001626] Phenanthrolines

*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]
NPO7688 Artemisia selengensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[Article]
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]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29460 Petiveria alliacea Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29428 Dalbergia cochinchinensis Species Fabaceae 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]
NPO19076 Gaillardia pulchella Species Asteraceae 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]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26775 Shorea wangtianshuea Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27125 Hovea linearis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9799 Hebeloma longicaudum Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29277 Lycopodium obscurum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19696 Othonna quercifolia Species Asteraceae 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]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18023 Vitex quinata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19234 Hymenopappus newberryi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15450 Minuria leptophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24832 Eriocaulon ligulatum Species Eriocaulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19298 Gerbera crocea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18518 Haematomma nemetzii Species Haematommataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25798 Gunnera perpensa Species Gunneraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27937 Centaurea iberica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19825 Litsea japonica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21360 Cordia corymbosa Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24978 Psila boliviensis Species Psilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18357 Euphorbia sanctae-catharinae Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22646 Malouetia tamaquarina Species Apocynaceae 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]
NPO24855 Callicarpa americana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7688 Artemisia selengensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26339 Dillenia philippinensis Species Dilleniaceae 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]
NPO19869 Fusicolla aquaeductuum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29522 Cuscuta salina Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29087 Ligularia brachyphylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24542 Doris obsoleta Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24225 Alexandrium peruvianum Species Gonyaulacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27361 Hylobius abietis Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29460 Petiveria alliacea Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26498 Vernonia cumingiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21044 Sphaerellopsis filum Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28418 Grateloupia filicina Species Halymeniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18499 Podium complanatum Species Sphecidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26989 Delphinium geyeri Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26662 Chrysanthemum foeniculaceum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29521 Genista purgans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17887 Penstemon centranthifolius Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11060 Doris luteorosea Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29247 Wahlenbergia marginata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28055 Perymenium berlandieri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19565 Crocus chrysanthus Species Iridaceae 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 NPC299954 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 NPC299954 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