Structure

Physi-Chem Properties

Molecular Weight:  342.12
Volume:  295.688
LogP:  -2.697
LogD:  -2.61
LogS:  -0.217
# Rotatable Bonds:  4
TPSA:  189.53
# H-Bond Aceptor:  11
# H-Bond Donor:  8
# Rings:  2
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.243
Synthetic Accessibility Score:  4.284
Fsp3:  1.0
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.112
MDCK Permeability:  0.00012418713595252484
Pgp-inhibitor:  0.01
Pgp-substrate:  0.931
Human Intestinal Absorption (HIA):  0.969
20% Bioavailability (F20%):  0.27
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.256
Plasma Protein Binding (PPB):  17.329835891723633%
Volume Distribution (VD):  0.376
Pgp-substrate:  63.587921142578125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.032
CYP2C19-inhibitor:  0.014
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.035
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.095
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  0.897
Half-life (T1/2):  0.842

ADMET: Toxicity

hERG Blockers:  0.339
Human Hepatotoxicity (H-HT):  0.053
Drug-inuced Liver Injury (DILI):  0.03
AMES Toxicity:  0.121
Rat Oral Acute Toxicity:  0.021
Maximum Recommended Daily Dose:  0.0
Skin Sensitization:  0.37
Carcinogencity:  0.025
Eye Corrosion:  0.003
Eye Irritation:  0.166
Respiratory Toxicity:  0.017

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  Natural Product: NPC304825

Natural Product ID:  NPC304825
Common Name*:   DLRVVLDZNNYCBX-LGHYCPABSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DLRVVLDZNNYCBX-LGHYCPABSA-N
Standard InCHI:  InChI=1S/C12H22O11/c13-1-3-5(14)8(17)10(19)12(23-3)21-2-4-6(15)7(16)9(18)11(20)22-4/h3-20H,1-2H2/t3-,4-,5+,6-,7+,8+,9+,10-,11+,12+/m1/s1
SMILES:  C([C@@H]1[C@@H]([C@@H]([C@H]([C@@H](OC[C@@H]2[C@H]([C@@H]([C@@H]([C@@H](O)O2)O)O)O)O1)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11724912
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002207] O-glycosyl compounds

*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
NPO17509 Gentiana bellidifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4020(01)98434-0]
NPO12113 Aconitum forrestii Species Ranunculaceae Eukaryota n.a. root n.a. DOI[10.1021/np50033a013]
NPO17406 Calophyllum lanigerum Species Calophyllaceae Eukaryota n.a. Sarawak, Malaysia n.a. PMID[11430019]
NPO17406 Calophyllum lanigerum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[1379639]
NPO12900 Sarcococca hookeriana Species Buxaceae Eukaryota n.a. whole plant n.a. PMID[17827771]
NPO14832 Calocedrus macrolepis Species Cupressaceae Eukaryota n.a. leaf n.a. PMID[18206367]
NPO12900 Sarcococca hookeriana Species Buxaceae Eukaryota n.a. whole plant n.a. PMID[18681480]
NPO12900 Sarcococca hookeriana Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[18681480]
NPO19447 Daphniphyllum subverticillatum Species Daphniphyllaceae Eukaryota leaves n.a. n.a. PMID[19739650]
NPO18442 Capsicum baccatum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[21535519]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. PMID[21625478]
NPO18682 Piper puberulum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[7623032]
NPO17406 Calophyllum lanigerum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[8792623]
NPO12113 Aconitum forrestii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8770 Euphorbia wallichii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18608 Fagopyrum cymosum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15880 Microlepia marginata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18682 Piper puberulum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8770 Euphorbia wallichii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12113 Aconitum forrestii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15880 Microlepia marginata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13433 Adenium obesum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18682 Piper puberulum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18608 Fagopyrum cymosum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16148 Neoboutonia glabrescens Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11662 Solanum virginianum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18608 Fagopyrum cymosum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18940 Selinum papyraceum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18442 Capsicum baccatum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13869 Ranunculus bulbosus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18540 Berkheya radula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8770 Euphorbia wallichii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2708 Agaricus nebularis Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19722 Tephrosia odorata Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14832 Calocedrus macrolepis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19447 Daphniphyllum subverticillatum Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17793 Parkia javanica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18608 Fagopyrum cymosum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19098 Hypotrachyna quaesita Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12113 Aconitum forrestii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9099 Carissa spinarum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16274 Calonectria lauri Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27385 Calamus insignis Species Sparidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12900 Sarcococca hookeriana Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18778 Paullinia pinnata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18682 Piper puberulum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19314 Albizia schimperana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13433 Adenium obesum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19249 Garcinia latissima Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22826 Buxus rolfei Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16148 Neoboutonia glabrescens Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15183 Salvia horminum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11331 Phellinus tremulae Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19842 Sideritis condensata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17648 Subergorgia hicksoni Species Subergorgiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10175 Anaptychia obscura Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18272 Mikania oblongifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19377 Podocarpus blumei Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16571 Canarium muelleri Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15880 Microlepia marginata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11662 Solanum virginianum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18361 Mollugo cerviana Species Molluginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17509 Gentiana bellidifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14266 Borassus flabellifer Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17406 Calophyllum lanigerum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18860 Pelea madagascarica Species Bovidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19849 Melilotus officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18064 Lycopodium paniculatum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20860 Lygodium pinnatifidum Species Lygodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19525 Tephrosia bracteolata Species Geometridae 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 NPC304825 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 NPC304825 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