Structure

Physi-Chem Properties

Molecular Weight:  311.14
Volume:  309.996
LogP:  -0.347
LogD:  4.791
LogS:  -1.679
# Rotatable Bonds:  7
TPSA:  123.93
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.516
Synthetic Accessibility Score:  4.401
Fsp3:  0.533
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.169
MDCK Permeability:  0.00010934232705039904
Pgp-inhibitor:  0.0
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.79
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.2
Plasma Protein Binding (PPB):  57.87406921386719%
Volume Distribution (VD):  0.415
Pgp-substrate:  47.150028228759766%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.028
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.808
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.123
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.008

ADMET: Excretion

Clearance (CL):  1.213
Half-life (T1/2):  0.784

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.348
Drug-inuced Liver Injury (DILI):  0.176
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.241
Maximum Recommended Daily Dose:  0.786
Skin Sensitization:  0.246
Carcinogencity:  0.348
Eye Corrosion:  0.004
Eye Irritation:  0.022
Respiratory Toxicity:  0.304

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  Natural Product: NPC103483

Natural Product ID:  NPC103483
Common Name*:   VZFRNCSOCOPNDB-UQJDIMSYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VZFRNCSOCOPNDB-UQJDIMSYSA-N
Standard InCHI:  InChI=1S/C15H21NO6/c1-8(4-3-5-9(2)14(19)20)11-7-16-13(15(21)22)10(11)6-12(17)18/h3-5,9-11,13,16H,6-7H2,1-2H3,(H,17,18)(H,19,20)(H,21,22)/b5-3+,8-4-/t9-,10-,11+,13-/m0/s1
SMILES:  C/C(=C/C=C/[C@H](C)C(=O)O)/[C@H]1CN[C@@H]([C@H]1CC(=O)O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5311075
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0001801] Kainoids

*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
NPO21005 Baphia nitida Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(92)80059-N]
NPO20931 Simaba multiflora Species Simaroubaceae Eukaryota n.a. xylem n.a. DOI[10.1016/S0040-4039(00)86970-1]
NPO4343 Guanomyces polythrix Species n.a. Eukaryota n.a. n.a. n.a. PMID[10869195]
NPO17256 Kobresia nepalensis Species Cyperaceae Eukaryota n.a. stem n.a. PMID[16508191]
NPO20931 Simaba multiflora Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[17340534]
NPO19192 Sinocalamus affinis Species n.a. n.a. n.a. stem n.a. PMID[21469695]
NPO19192 Sinocalamus affinis Species n.a. n.a. skin-removed stems Pingle Town, Sichuang Province, China 2008-AUG PMID[21469695]
NPO19192 Sinocalamus affinis Species n.a. n.a. n.a. n.a. n.a. PMID[22690646]
NPO19901 Emilia sonchifolia Species Asteraceae Eukaryota n.a. aerial part n.a. PMID[23397723]
NPO20739 Jungermannia hyalina Species Jungermanniaceae Eukaryota n.a. Guangxi Zhuang Autonomous Region, China n.a. PMID[25856683]
NPO21618 Ircinia oros Species Irciniidae Eukaryota n.a. n.a. n.a. PMID[28840725]
NPO21679 Nuphar lutea Species Nymphaeaceae Eukaryota n.a. n.a. n.a. PMID[31182315]
NPO20212 Callistemon viminalis Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[31276403]
NPO20931 Simaba multiflora Species Simaroubaceae Eukaryota Fruits n.a. n.a. PMID[3760884]
NPO20931 Simaba multiflora Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[6736970]
NPO20931 Simaba multiflora Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[6875576]
NPO20931 Simaba multiflora Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[6875577]
NPO20931 Simaba multiflora Species Simaroubaceae Eukaryota n.a. xylem n.a. PMID[6875577]
NPO20671 Selliguea feei Species Polypodiaceae Eukaryota Rhizomes n.a. n.a. PMID[8254348]
NPO21679 Nuphar lutea Species Nymphaeaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19017 Prangos pabularia Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8650.1 Perilla frutescens var. arguta Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19488 Trifolium subterraneum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19901 Emilia sonchifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19017 Prangos pabularia Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19488 Trifolium subterraneum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17256 Kobresia nepalensis Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19901 Emilia sonchifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21679 Nuphar lutea Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11966 Euphorbia kamerunica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8678 Trillium camschatcense Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8650.1 Perilla frutescens var. arguta Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19901 Emilia sonchifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19017 Prangos pabularia Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14466 Penicillium olsonii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20546 Cissus pallidiflorus Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17256 Kobresia nepalensis Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21426 Alstroemeria revoluta Species Alstroemeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21486 Marrubium alysson Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21289 Teucrium oxylepis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21231 Astragalus tragacantha Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18096 Excoecaria oppositifolia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19622 Euphorbia marginata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26840 Litsea aciculata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20931 Simaba multiflora Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19901 Emilia sonchifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19192 Sinocalamus affinis Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO20671 Selliguea feei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21088 Litsea pulchella Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2854 Gymnosporia senegalensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21365 Ligularia muliensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8650.1 Perilla frutescens var. arguta Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20813 Myrmica sabuleti Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17515 Pronephrium triphyllum Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3777 Stevia chamaedrys Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20051 Gardenia collinsae Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21679 Nuphar lutea Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19017 Prangos pabularia Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19986 Crataegus davisii Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11622.1 Shuteria involucrata var. vestita Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3237 Mytilus edulis Species Mytilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21618 Ircinia oros Species Irciniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16907 Pentzia incana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15216 Encephalartos altensteinii Species Zamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4343 Guanomyces polythrix Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20212 Callistemon viminalis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14136 Acherontia atropus Species Sphingidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14330 Agave aurea Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16454 Crinum erubescens Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18620 Grindelia acutifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20612 Ursinia abrotanifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16044 Cupressus lawsoniana Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19488 Trifolium subterraneum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20739 Jungermannia hyalina Species Jungermanniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11966 Euphorbia kamerunica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20408 Ajuga spectabilis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13260 Eria foetida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20872 Melampodium heterophyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19773 Xenorhabdus bovienii Species Morganellaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO21005 Baphia nitida Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22510 Eupatorium havanense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21550 Achillea macrophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8678 Trillium camschatcense Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20340 Pausinystalia mayumbensis Species Rubiaceae 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 NPC103483 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 NPC103483 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