Structure

Physi-Chem Properties

Molecular Weight:  342.13
Volume:  327.955
LogP:  -0.41
LogD:  -0.424
LogS:  -1.03
# Rotatable Bonds:  6
TPSA:  128.84
# H-Bond Aceptor:  8
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.44
Synthetic Accessibility Score:  3.63
Fsp3:  0.5
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:  -5.634
MDCK Permeability:  9.736734500620514e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.049
Human Intestinal Absorption (HIA):  0.773
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.969

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.294
Plasma Protein Binding (PPB):  50.75629425048828%
Volume Distribution (VD):  0.418
Pgp-substrate:  36.069610595703125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.064
CYP1A2-substrate:  0.092
CYP2C19-inhibitor:  0.013
CYP2C19-substrate:  0.599
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.056
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.108
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.053

ADMET: Excretion

Clearance (CL):  3.764
Half-life (T1/2):  0.902

ADMET: Toxicity

hERG Blockers:  0.091
Human Hepatotoxicity (H-HT):  0.282
Drug-inuced Liver Injury (DILI):  0.738
AMES Toxicity:  0.337
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.113
Carcinogencity:  0.142
Eye Corrosion:  0.004
Eye Irritation:  0.093
Respiratory Toxicity:  0.012

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  Natural Product: NPC300969

Natural Product ID:  NPC300969
Common Name*:   SFLMUHDGSQZDOW-JNDSXIQISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SFLMUHDGSQZDOW-JNDSXIQISA-N
Standard InCHI:  InChI=1S/C16H22O8/c1-22-11-7-9(3-2-6-17)4-5-10(11)23-16-15(21)14(20)13(19)12(8-18)24-16/h2-5,7,12-21H,6,8H2,1H3/b3-2-/t12-,13-,14+,15-,16-/m1/s1
SMILES:  COc1cc(/C=CCO)ccc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   91895380
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:0004165] Phenolic glycosides

*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
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(01)00320-X]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. leaf n.a. PMID[11738417]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. root n.a. PMID[16335823]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[19245261]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20151678]
NPO6964 Cistanche tubulosa Species Orobanchaceae Eukaryota fresh stems n.a. n.a. PMID[20159656]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20853876]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. fruit n.a. PMID[21462031]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. root n.a. PMID[22233034]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. PMID[25900014]
NPO8500 Acanthopanax gracilistylus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32319765]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[33052051]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. root n.a. PMID[9397205]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6964 Cistanche tubulosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21166 Kalopanax septemlobus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20352 Gentiana straminea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8500 Acanthopanax gracilistylus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21166 Kalopanax septemlobus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6964 Cistanche tubulosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20352 Gentiana straminea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8500 Acanthopanax gracilistylus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO753 Acanthopanax sessiliflorum n.a. n.a. n.a. n.a. n.a. n.a. Database[TM-MC]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20352 Gentiana straminea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26538 Phellodendron chinese Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21166 Kalopanax septemlobus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6964 Cistanche tubulosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6964 Cistanche tubulosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8500 Acanthopanax gracilistylus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22686 Gentiana macrophylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21166 Kalopanax septemlobus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20352 Gentiana straminea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae 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 NPC300969 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 NPC300969 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