Structure

Physi-Chem Properties

Molecular Weight:  234.21
Volume:  255.764
LogP:  2.756
LogD:  2.679
LogS:  -1.887
# Rotatable Bonds:  0
TPSA:  6.48
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.635
Synthetic Accessibility Score:  4.281
Fsp3:  1.0
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:  -4.794
MDCK Permeability:  1.0664014553185552e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.984
30% Bioavailability (F30%):  0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.914
Plasma Protein Binding (PPB):  29.23182487487793%
Volume Distribution (VD):  2.865
Pgp-substrate:  70.96910095214844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.112
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.935
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.033
CYP2D6-inhibitor:  0.972
CYP2D6-substrate:  0.905
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.716

ADMET: Excretion

Clearance (CL):  15.322
Half-life (T1/2):  0.207

ADMET: Toxicity

hERG Blockers:  0.669
Human Hepatotoxicity (H-HT):  0.365
Drug-inuced Liver Injury (DILI):  0.867
AMES Toxicity:  0.046
Rat Oral Acute Toxicity:  0.104
Maximum Recommended Daily Dose:  0.143
Skin Sensitization:  0.966
Carcinogencity:  0.53
Eye Corrosion:  0.976
Eye Irritation:  0.899
Respiratory Toxicity:  0.946

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  Natural Product: NPC228980

Natural Product ID:  NPC228980
Common Name*:   SLRCCWJSBJZJBV-ZQDZILKHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SLRCCWJSBJZJBV-ZQDZILKHSA-N
Standard InCHI:  InChI=1S/C15H26N2/c1-3-7-16-11-13-9-12(14(16)5-1)10-17-8-4-2-6-15(13)17/h12-15H,1-11H2/t12-,13-,14-,15+/m0/s1
SMILES:  C1CC[C@@H]2N(C1)C[C@@H]1C[C@H]2CN2[C@@H]1CCCC2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1908847
PubChem CID:   644020
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0001795] Sparteine, lupanine, and related alkaloids

*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
NPO24195 Stylissa carteri Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[15043426]
NPO25980 Rhododendron molle Species Ericaceae Eukaryota flowers n.a. n.a. PMID[15974620]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21574561]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23747095]
NPO3866 Pistia stratiotes Species Araceae Eukaryota n.a. n.a. n.a. PMID[24258601]
NPO25980 Rhododendron molle Species Ericaceae Eukaryota Roots n.a. n.a. PMID[26599832]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29192771]
NPO25980 Rhododendron molle Species Ericaceae Eukaryota Leaves n.a. n.a. PMID[29272126]
NPO24195 Stylissa carteri Species Axinellidae Eukaryota n.a. indopacific n.a. PMID[9917317]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Shoot Essent. Oil n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25980 Rhododendron molle Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21685 Magnolia coco Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO25980 Rhododendron molle Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21685 Magnolia coco Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21685 Magnolia coco Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25980 Rhododendron molle Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25980 Rhododendron molle Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2342 Cytisus scoparius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21102 Thalictrum wangii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2502 Lupinus mexicanus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24195 Stylissa carteri Species Axinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16529 Plagiodera versicolora Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12511 Leplaea thompsonii Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3866 Pistia stratiotes Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21982 Erechtites hieraciifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25980 Rhododendron molle Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5390 Lupinus pusillus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21685 Magnolia coco Species Magnoliaceae 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
NPT616 Cell Line MDCK Canis lupus familiaris CC50 > 80000.0 nM PMID[557047]
NPT197 Protein-Protein Interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 39810.7 nM PMID[557046]
NPT1453 Organism Influenza A virus (A/PR/8/34(H1N1)) Influenza A virus (A/Puerto Rico/8/1934(H1N1)) EC50 = 19700.0 nM PMID[557047]
NPT2 Others Unspecified AC50 n.a. 631.0 nM PMID[557048]
NPT2 Others Unspecified Ac50 n.a. 28.18 uM PMID[557048]
NPT2 Others Unspecified Ac50 n.a. 0.631 uM PMID[557048]
NPT2 Others Unspecified Ac50 n.a. 39.81 uM PMID[557048]
NPT2 Others Unspecified AC50 n.a. 28183.8 nM PMID[557048]
NPT2 Others Unspecified AC50 n.a. 39810.7 nM PMID[557048]
NPT2 Others Unspecified Potency n.a. 8109.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 45.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 23710.1 nM PubChem BioAssay data set

☑ 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 NPC228980 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
1.0 High Similarity NPC243635
1.0 High Similarity NPC151004
0.75 Intermediate Similarity NPC290231
0.75 Intermediate Similarity NPC266383
0.75 Intermediate Similarity NPC68043
0.75 Intermediate Similarity NPC48448
0.75 Intermediate Similarity NPC180401
0.75 Intermediate Similarity NPC206241
0.75 Intermediate Similarity NPC271803
0.7059 Intermediate Similarity NPC17770
0.6957 Remote Similarity NPC80447
0.6618 Remote Similarity NPC127553
0.6618 Remote Similarity NPC255050
0.6301 Remote Similarity NPC308050
0.625 Remote Similarity NPC112398
0.6234 Remote Similarity NPC124359
0.6234 Remote Similarity NPC153734
0.6207 Remote Similarity NPC201713
0.619 Remote Similarity NPC231129
0.6133 Remote Similarity NPC120699
0.6133 Remote Similarity NPC127430
0.6133 Remote Similarity NPC268580
0.6094 Remote Similarity NPC82919
0.6 Remote Similarity NPC39308
0.5926 Remote Similarity NPC168017
0.5921 Remote Similarity NPC90839
0.5897 Remote Similarity NPC255430
0.5849 Remote Similarity NPC471440
0.5849 Remote Similarity NPC471575
0.5783 Remote Similarity NPC178632
0.5769 Remote Similarity NPC31313
0.5769 Remote Similarity NPC149908
0.5769 Remote Similarity NPC45906
0.5769 Remote Similarity NPC288415
0.5763 Remote Similarity NPC153803
0.575 Remote Similarity NPC143344
0.575 Remote Similarity NPC135639
0.575 Remote Similarity NPC234822
0.575 Remote Similarity NPC78058
0.575 Remote Similarity NPC61321
0.575 Remote Similarity NPC207048
0.5696 Remote Similarity NPC93630
0.5606 Remote Similarity NPC21781

  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 NPC228980 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
1.0 High Similarity NPD1823 Approved
1.0 High Similarity NPD1822 Approved
1.0 High Similarity NPD1821 Approved
0.7818 Intermediate Similarity NPD3727 Discontinued
0.661 Remote Similarity NPD3711 Phase 3
0.661 Remote Similarity NPD3712 Phase 3
0.6552 Remote Similarity NPD3721 Approved
0.6552 Remote Similarity NPD3722 Approved
0.6379 Remote Similarity NPD5793 Discontinued
0.5932 Remote Similarity NPD4834 Discontinued
0.5902 Remote Similarity NPD4839 Approved
0.5862 Remote Similarity NPD5379 Clinical (unspecified phase)
0.5818 Remote Similarity NPD390 Approved
0.5818 Remote Similarity NPD718 Approved
0.5625 Remote Similarity NPD298 Clinical (unspecified phase)

  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