Structure

Physi-Chem Properties

Molecular Weight:  297.12
Volume:  292.7
LogP:  -1.195
LogD:  3.591
LogS:  -1.606
# 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:  0.51
Synthetic Accessibility Score:  4.202
Fsp3:  0.5
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:  -6.207
MDCK Permeability:  3.783728607231751e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.734
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.144
Plasma Protein Binding (PPB):  35.71917724609375%
Volume Distribution (VD):  0.418
Pgp-substrate:  57.28138732910156%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.024
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.039
CYP2C9-inhibitor:  0.022
CYP2C9-substrate:  0.922
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.147
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.009

ADMET: Excretion

Clearance (CL):  1.531
Half-life (T1/2):  0.802

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.317
Drug-inuced Liver Injury (DILI):  0.049
AMES Toxicity:  0.002
Rat Oral Acute Toxicity:  0.137
Maximum Recommended Daily Dose:  0.892
Skin Sensitization:  0.271
Carcinogencity:  0.465
Eye Corrosion:  0.041
Eye Irritation:  0.044
Respiratory Toxicity:  0.223

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC210491

Natural Product ID:  NPC210491
Common Name*:   DMRLVPYGNHGWOO-ZKRDDCEXSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DMRLVPYGNHGWOO-ZKRDDCEXSA-N
Standard InCHI:  InChI=1S/C14H19NO6/c1-8(4-2-3-5-11(16)17)10-7-15-13(14(20)21)9(10)6-12(18)19/h2-4,9-10,13,15H,5-7H2,1H3,(H,16,17)(H,18,19)(H,20,21)/p-2/b3-2+,8-4+/t9-,10+,13-/m0/s1
SMILES:  C/C(=CC=CCC(=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:   n.a.
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
NPO28122 Senecio chionophilus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[15387646]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28645 Chondria armata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28645 Chondria armata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28493 Euphorbia cuneata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27701 Otholobium glandulosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21945 Amomum melegueta Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28539 Xestospongia vanilla Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28314 Hakea trifurcata Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27768 Terminalia brachystemma Species Combretaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28645 Chondria armata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27849 Raoulia australis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27917 Ulmus campestris Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12214 Leontice robustum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28505 Arum palaestinum Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28279 Mikania cordifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28030 Polysiphonia nigra Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28227 Prunus speciosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27889 Anacyclus monanthos Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28403 Comanthus bennetti Species Comatulidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28420 Guizotia scabra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27969 Elvira biflora Species Trochilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28156 Nezara viridula Species Pentatomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28122 Senecio chionophilus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28082 Corydalis tashiroi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28522 Flustra denticulata Species Flustridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28331 Astragalus siculus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28105 Coriolopsis gallica Species Coriolaceae 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 NPC210491 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 NPC210491 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