Structure

Physi-Chem Properties

Molecular Weight:  372.19
Volume:  391.531
LogP:  4.327
LogD:  3.814
LogS:  -4.956
# Rotatable Bonds:  6
TPSA:  46.15
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.728
Synthetic Accessibility Score:  3.194
Fsp3:  0.455
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.766
MDCK Permeability:  7.070942228892818e-05
Pgp-inhibitor:  0.996
Pgp-substrate:  0.075
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.167
30% Bioavailability (F30%):  0.659

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.15
Plasma Protein Binding (PPB):  83.81059265136719%
Volume Distribution (VD):  1.179
Pgp-substrate:  5.265468120574951%

ADMET: Metabolism

CYP1A2-inhibitor:  0.05
CYP1A2-substrate:  0.967
CYP2C19-inhibitor:  0.874
CYP2C19-substrate:  0.903
CYP2C9-inhibitor:  0.817
CYP2C9-substrate:  0.837
CYP2D6-inhibitor:  0.097
CYP2D6-substrate:  0.935
CYP3A4-inhibitor:  0.935
CYP3A4-substrate:  0.87

ADMET: Excretion

Clearance (CL):  10.551
Half-life (T1/2):  0.263

ADMET: Toxicity

hERG Blockers:  0.218
Human Hepatotoxicity (H-HT):  0.112
Drug-inuced Liver Injury (DILI):  0.928
AMES Toxicity:  0.175
Rat Oral Acute Toxicity:  0.1
Maximum Recommended Daily Dose:  0.035
Skin Sensitization:  0.691
Carcinogencity:  0.154
Eye Corrosion:  0.005
Eye Irritation:  0.182
Respiratory Toxicity:  0.238

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  Natural Product: NPC93850

Natural Product ID:  NPC93850
Common Name*:   JLJAVUZBHSLLJL-GKHNXXNSSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JLJAVUZBHSLLJL-GKHNXXNSSA-N
Standard InCHI:  InChI=1S/C22H28O5/c1-13-14(2)22(16-8-10-18(24-4)20(12-16)26-6)27-21(13)15-7-9-17(23-3)19(11-15)25-5/h7-14,21-22H,1-6H3/t13-,14-,21-,22+/m0/s1
SMILES:  C[C@H]1[C@H](C)[C@H](c2ccc(c(c2)OC)OC)O[C@@H]1c1ccc(c(c1)OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   443026
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0003686] Furanoid lignans
        • [CHEMONTID:0001604] Tetrahydrofuran lignans
          • [CHEMONTID:0003423] 7,7'-epoxylignans

*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
NPO7850 Schisandra propinqua Species Schisandraceae Eukaryota n.a. stem n.a. DOI[10.1002/cjoc.20010190319]
NPO7850 Schisandra propinqua Species Schisandraceae Eukaryota n.a. stem n.a. DOI[10.1016/j.tet.2008.10.079]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4039(01)99818-1]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[11040054]
NPO7850 Schisandra propinqua Species Schisandraceae Eukaryota n.a. stem n.a. PMID[11395273]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. PMID[11421725]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. PMID[15165135]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[16724856]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. leaf n.a. PMID[17999353]
NPO7850 Schisandra propinqua Species Schisandraceae Eukaryota n.a. stem n.a. PMID[18536373]
NPO7850 Schisandra propinqua Species Schisandraceae Eukaryota aerial parts Erlang Mountain area of Sichuan Province, China 2007-SEP PMID[19413342]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota Roots; Tubers n.a. n.a. PMID[19639966]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[19900811]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. PMID[20476749]
NPO7850 Schisandra propinqua Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[20681569]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota Rhizomes n.a. n.a. PMID[21936523]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota n.a. rhizome n.a. PMID[21936523]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota rhizomes n.a. n.a. PMID[22951040]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. rhizome n.a. PMID[23713285]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota rhizomes n.a. n.a. PMID[26296476]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. PMID[26305406]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota Rhizomes n.a. n.a. PMID[29116780]
NPO9925 Rhododendron latoucheae Species Ericaceae Eukaryota Twigs; Leaves n.a. n.a. PMID[30106288]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. aerial part n.a. PMID[8237383]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[8237383]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[8368081]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9480 Huperzia miyoshiana Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9480 Huperzia miyoshiana Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7850 Schisandra propinqua Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2894 Mycena viridimarginata Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9925 Rhododendron latoucheae Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7374 Seseli montanum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6475 Gymnosporia trigyna Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5700 Mortonia hidalgensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7850 Schisandra propinqua Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19174 Anoplophora chinensis Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9480 Huperzia miyoshiana Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9834 Veronica austriaca Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6903 Lecanora straminea Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7522 Streptomyces amakusaensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6666 Eremanthus incanus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11167 Prunus ssiori Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9571 Pseudobrickellia brasiliensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO313 Castilleja sulphurea Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7128 Cynthia savignyi n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9301 Dioscorea sativa Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1155 Forsythia japonica Species Oleaceae 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
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 = 2300.0 nM PMID[568470]

☑ 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 NPC93850 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 NPC93850 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