Structure

Physi-Chem Properties

Molecular Weight:  302.08
Volume:  293.909
LogP:  2.442
LogD:  2.287
LogS:  -3.666
# Rotatable Bonds:  2
TPSA:  96.22
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.787
Synthetic Accessibility Score:  3.031
Fsp3:  0.188
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:  -4.838
MDCK Permeability:  9.058812793227844e-06
Pgp-inhibitor:  0.009
Pgp-substrate:  0.082
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.897
30% Bioavailability (F30%):  0.972

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.03
Plasma Protein Binding (PPB):  97.36373901367188%
Volume Distribution (VD):  0.554
Pgp-substrate:  2.516343593597412%

ADMET: Metabolism

CYP1A2-inhibitor:  0.965
CYP1A2-substrate:  0.871
CYP2C19-inhibitor:  0.479
CYP2C19-substrate:  0.074
CYP2C9-inhibitor:  0.684
CYP2C9-substrate:  0.948
CYP2D6-inhibitor:  0.725
CYP2D6-substrate:  0.888
CYP3A4-inhibitor:  0.869
CYP3A4-substrate:  0.258

ADMET: Excretion

Clearance (CL):  13.252
Half-life (T1/2):  0.68

ADMET: Toxicity

hERG Blockers:  0.069
Human Hepatotoxicity (H-HT):  0.096
Drug-inuced Liver Injury (DILI):  0.625
AMES Toxicity:  0.396
Rat Oral Acute Toxicity:  0.492
Maximum Recommended Daily Dose:  0.443
Skin Sensitization:  0.882
Carcinogencity:  0.17
Eye Corrosion:  0.003
Eye Irritation:  0.749
Respiratory Toxicity:  0.133

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  Natural Product: NPC308379

Natural Product ID:  NPC308379
Common Name*:   VODZWHSRITUHNI-LLVKDONJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VODZWHSRITUHNI-LLVKDONJSA-N
Standard InCHI:  InChI=1S/C16H14O6/c1-21-13-5-8(17)2-3-10(13)11-7-22-14-6-9(18)4-12(19)15(14)16(11)20/h2-6,11,17-19H,7H2,1H3/t11-/m1/s1
SMILES:  COc1cc(ccc1[C@H]1COc2cc(cc(c2C1=O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0002586] O-methylated isoflavonoids
          • [CHEMONTID:0002604] 2'-O-methylated isoflavonoids

*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
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[11374966]
NPO2280 Streptomyces griseochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[12964155]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16038550]
NPO11789 Swertia decussata Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[16286309]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17583950]
NPO733 Pseudoceratina arabica Species Pseudoceratinidae Eukaryota n.a. Red Sea n.a. PMID[18598078]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18855446]
NPO2280 Streptomyces griseochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[19191560]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20455578]
NPO12644 Lunularia cruciata Species Lunulariaceae Eukaryota n.a. n.a. n.a. PMID[21625478]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21775156]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23286284]
NPO2280 Streptomyces griseochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[23377931]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24108414]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25620156]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27569393]
NPO4734 Syzygium nervosum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[27797185]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29185738]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30351923]
NPO12644 Lunularia cruciata Species Lunulariaceae Eukaryota n.a. n.a. n.a. PMID[30848895]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[3655791]
NPO17794 Streptomyces violaceusniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[8557611]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota roots n.a. n.a. PMID[9834151]
NPO26606 Macadamia ternifolia Species Proteaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7001 Berberis floribunda Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4002 Lappula intermedia Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24178 Citrus rugulosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18560 Tripterospermum japonicum Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24178 Citrus rugulosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8701 Bonamia spectabilis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7001 Berberis floribunda Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26606 Macadamia ternifolia Species Proteaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7319 Jamesoniella colorata Species Jungermanniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18560 Tripterospermum japonicum Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4002 Lappula intermedia Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9452 Pulsatilla campanella Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4734 Syzygium nervosum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4910 Lepidosperma ustulatum Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17794 Streptomyces violaceusniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO9009 Atuna racemosa Species Chrysobalanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19587 Cordia rothii Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11789 Swertia decussata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2565 Aglaia australiensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7949 Pterodon emarginatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19809 Streptomyces roseoviolaceus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8398 Cymodocea nodosa Species Cymodoceaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24178 Citrus rugulosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26606 Macadamia ternifolia Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10546 Allagopappus viscosissimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7627 Fumaria micrantha Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11910 Peltogyne pubescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12644 Lunularia cruciata Species Lunulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9452 Pulsatilla campanella Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12864 Trogoderma granarium Species Dermestidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9226 Astragalus pycnanthus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2280 Streptomyces griseochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO3311 Diplacus longiflorus Species Phrymaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23899 Rosulabryum capillare Species Bryaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4002 Lappula intermedia Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO733 Pseudoceratina arabica Species Pseudoceratinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11534 Astragalus spinosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9811 Macrotyloma uniflorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14323 Bossiella orbigniana Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19260 Zanthoxylum petiolare Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12920 Erimacrus isenbeckii Species Atelecyclidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18560 Tripterospermum japonicum Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12169 Ranunculus peltatus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7319 Jamesoniella colorata Species Jungermanniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3658 Achillea pseudopectinata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6572 Dunalia solanacea Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7001 Berberis floribunda Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11223 Pleurotus japonicus Species Pleurotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8701 Bonamia spectabilis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9640 Dinophysis fortii Species Dinophysiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18447 Papaver tatricum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8006 Berlinia tomentosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12284 Hydrangea serrata Species Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15439 Iyengaria stellata Species Scytosiphonaceae 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 NPC308379 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 NPC308379 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