Structure

Physi-Chem Properties

Molecular Weight:  552.21
Volume:  578.459
LogP:  6.345
LogD:  4.528
LogS:  -3.122
# Rotatable Bonds:  9
TPSA:  116.45
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  5
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.17
Synthetic Accessibility Score:  3.736
Fsp3:  0.206
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.123
MDCK Permeability:  1.1485190952953417e-05
Pgp-inhibitor:  0.277
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.715
30% Bioavailability (F30%):  0.947

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.025
Plasma Protein Binding (PPB):  99.70252990722656%
Volume Distribution (VD):  0.58
Pgp-substrate:  0.8239691853523254%

ADMET: Metabolism

CYP1A2-inhibitor:  0.501
CYP1A2-substrate:  0.306
CYP2C19-inhibitor:  0.962
CYP2C19-substrate:  0.057
CYP2C9-inhibitor:  0.948
CYP2C9-substrate:  0.985
CYP2D6-inhibitor:  0.721
CYP2D6-substrate:  0.923
CYP3A4-inhibitor:  0.777
CYP3A4-substrate:  0.262

ADMET: Excretion

Clearance (CL):  13.461
Half-life (T1/2):  0.59

ADMET: Toxicity

hERG Blockers:  0.601
Human Hepatotoxicity (H-HT):  0.112
Drug-inuced Liver Injury (DILI):  0.075
AMES Toxicity:  0.064
Rat Oral Acute Toxicity:  0.132
Maximum Recommended Daily Dose:  0.835
Skin Sensitization:  0.965
Carcinogencity:  0.433
Eye Corrosion:  0.003
Eye Irritation:  0.767
Respiratory Toxicity:  0.174

Download Data

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

  Natural Product: NPC251656

Natural Product ID:  NPC251656
Common Name*:   FBPFZTCFMRRESA-ZXXMMSQZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FBPFZTCFMRRESA-ZXXMMSQZSA-N
Standard InCHI:  InChI=1S/C6H14O6/c7-1-3(9)5(11)6(12)4(10)2-8/h3-12H,1-2H2/t3-,4-,5+,6+/m1/s1
SMILES:  C([C@H]([C@@H]([C@H]([C@@H](CO)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   90540
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002210] Sugar alcohols

*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
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. DOI[10.1007/s11306-014-0728-9]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1038/sdata.2014.29]
NPO19009 Ipomoea orizabensis Species Convolvulaceae Eukaryota Roots Mexican n.a. PMID[10479311]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[11171227]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12576668]
NPO19009 Ipomoea orizabensis Species Convolvulaceae Eukaryota crude resin Mexican n.a. PMID[16562846]
NPO14026.1 Vitex negundo var. cannabifolia Varieties Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25245917]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. seed n.a. PMID[25891114]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8987503]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. Database[MetaboLights]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18614 Gentiana turkestanorum Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14033 Torilis arvensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4243 Didymocarpus leucocalyx Species Gesneriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14026.1 Vitex negundo var. cannabifolia Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20473 Vaccinium membranaceum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16442 Omphalia campanella n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO19009 Ipomoea orizabensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18614 Gentiana turkestanorum Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19772 Ceroplastes ceriferus Species Coccidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20669 Baccharis rhetinodes Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21549 Consolida raveyi Species Ranunculaceae 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 NPC251656 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 NPC251656 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