Structure

Physi-Chem Properties

Molecular Weight:  329.11
Volume:  304.36
LogP:  -0.335
LogD:  -0.048
LogS:  -1.43
# Rotatable Bonds:  6
TPSA:  142.52
# H-Bond Aceptor:  9
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.372
Synthetic Accessibility Score:  3.663
Fsp3:  0.571
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:  -5.414
MDCK Permeability:  0.0002649313537403941
Pgp-inhibitor:  0.003
Pgp-substrate:  0.022
Human Intestinal Absorption (HIA):  0.847
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.902

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.203
Plasma Protein Binding (PPB):  72.8668212890625%
Volume Distribution (VD):  0.747
Pgp-substrate:  17.85227394104004%

ADMET: Metabolism

CYP1A2-inhibitor:  0.107
CYP1A2-substrate:  0.043
CYP2C19-inhibitor:  0.071
CYP2C19-substrate:  0.569
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.564
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.363
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.065

ADMET: Excretion

Clearance (CL):  2.463
Half-life (T1/2):  0.738

ADMET: Toxicity

hERG Blockers:  0.402
Human Hepatotoxicity (H-HT):  0.304
Drug-inuced Liver Injury (DILI):  0.026
AMES Toxicity:  0.08
Rat Oral Acute Toxicity:  0.547
Maximum Recommended Daily Dose:  0.029
Skin Sensitization:  0.802
Carcinogencity:  0.801
Eye Corrosion:  0.004
Eye Irritation:  0.136
Respiratory Toxicity:  0.086

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  Natural Product: NPC310532

Natural Product ID:  NPC310532
Common Name*:   JRSACOBIDKCJGV-RKQHYHRCSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JRSACOBIDKCJGV-RKQHYHRCSA-N
Standard InCHI:  InChI=1S/C14H19NO8/c16-7-10-11(17)12(18)13(19)14(23-10)22-9-3-1-8(2-4-9)5-6-15(20)21/h1-4,10-14,16-19H,5-7H2/t10-,11-,12+,13-,14-/m1/s1
SMILES:  c1cc(ccc1CCN(=O)=O)O[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:   21629843
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
NPO19242 Eucalyptus albens Species Myrtaceae Eukaryota flowers n.a. n.a. PMID[10075775]
NPO11164 Renealmia alpinia Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[10479331]
NPO19436 Annona cherimola Species Annonaceae Eukaryota Seeds n.a. n.a. PMID[15387664]
NPO19083 Alstonia angustiloba Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[18524603]
NPO17759 Rhododendron mucronulatum Species Ericaceae Eukaryota n.a. stem n.a. PMID[21443171]
NPO18602 Melampodium leucanthum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO18602 Melampodium leucanthum Species Asteraceae Eukaryota leaves and branches San Antonio, Texas 2004-JUN PMID[25685941]
NPO18602 Melampodium leucanthum Species Asteraceae Eukaryota leaves and branches n.a. n.a. PMID[25685941]
NPO17296 Beesia calthifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[26238319]
NPO18676 Clerodendrum trichotomum Species Lamiaceae Eukaryota Roots n.a. n.a. PMID[29924604]
NPO11164 Renealmia alpinia Species Zingiberaceae Eukaryota n.a. Suriname rainforest n.a. PMID[9428162]
NPO19436 Annona cherimola Species Annonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19436 Annona cherimola Species Annonaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO19436 Annona cherimola Species Annonaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO19436 Annona cherimola Species Annonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23797 Skimmia reevesiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17759 Rhododendron mucronulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1783 Euonymus fortunei Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18765 Juniperus scopulorum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19769 Boschniakia rossica Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13737 Tephroseris kirilowii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17296 Beesia calthifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14233 Ormosia dasycarpa Species Limoniidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24402.1 Coffea liberica var. dewevrei Varieties Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18676 Clerodendrum trichotomum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23797 Skimmia reevesiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17759 Rhododendron mucronulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19769 Boschniakia rossica Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13358 Piper brachystachyum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1783 Euonymus fortunei Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13737 Tephroseris kirilowii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18765 Juniperus scopulorum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11967 Delphinium giraldii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19769 Boschniakia rossica Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18765 Juniperus scopulorum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23797 Skimmia reevesiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17759 Rhododendron mucronulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19709 Pseudocyphellaria australiensis Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4679 Hedysarum gmelini Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19242 Eucalyptus albens Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17499 Bursera kerberi Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13358 Piper brachystachyum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9906 Zephyranthes flava Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19371 Costasiella ocellifera Species Costasiellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18348 Crotalaria stolzii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17114 Streptomyces melanogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO18048 Phlomis crinita Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8172 Emericellopsis minima Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16135 Pestalotiopsis oenotherae Species Sporocadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17630 Helenium integrifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18533 Delisea elegans Species Bonnemaisoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19769 Boschniakia rossica Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15802 Papaver pseudocanescens Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO968 Artemisia pectinata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5455 Euploca racemosa Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19170 Lasianthaea podocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18169 Creosphaeria sassafras Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25370 Botrychium ternatum Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23797 Skimmia reevesiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24402.1 Coffea liberica var. dewevrei Varieties Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1783 Euonymus fortunei Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29450 Streptomyces parvisporogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12223 Stellaria media Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19083 Alstonia angustiloba Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16325 Sideritis dasygnaphala Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12870 Curcuma aeruginosa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24507 Kalmia angustifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19572 Pellacalyx axillaris Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19436 Annona cherimola Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14233 Ormosia dasycarpa Species Limoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18765 Juniperus scopulorum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11967 Delphinium giraldii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18602 Melampodium leucanthum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16981 Gutierrezia dracunculoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18424 Selinum libanotis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11646 Morella pensylvanica Species Myricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15127 Senecio congestus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18927 Clinacanthus nutans Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12914 Sarcophyton flexuosum Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18262 Aspergillus microcysticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29531 Lupinus cosentinii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17296 Beesia calthifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18676 Clerodendrum trichotomum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17354 Micromonospora echinospora Species Micromonosporaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11164 Renealmia alpinia Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11081 Baccharis grandicapitulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13737 Tephroseris kirilowii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17759 Rhododendron mucronulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17230 Psidium acutangulum Species Myrtaceae 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 NPC310532 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 NPC310532 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