Structure

Physi-Chem Properties

Molecular Weight:  516.31
Volume:  547.479
LogP:  4.96
LogD:  4.455
LogS:  -4.897
# Rotatable Bonds:  11
TPSA:  95.97
# H-Bond Aceptor:  7
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.182
Synthetic Accessibility Score:  5.185
Fsp3:  0.733
Lipinski Rule-of-5:  Accepted
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:  -4.83
MDCK Permeability:  1.9737206457648426e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.956
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.972
Plasma Protein Binding (PPB):  81.34114074707031%
Volume Distribution (VD):  0.919
Pgp-substrate:  19.356908798217773%

ADMET: Metabolism

CYP1A2-inhibitor:  0.043
CYP1A2-substrate:  0.074
CYP2C19-inhibitor:  0.494
CYP2C19-substrate:  0.169
CYP2C9-inhibitor:  0.86
CYP2C9-substrate:  0.091
CYP2D6-inhibitor:  0.111
CYP2D6-substrate:  0.049
CYP3A4-inhibitor:  0.924
CYP3A4-substrate:  0.525

ADMET: Excretion

Clearance (CL):  5.348
Half-life (T1/2):  0.545

ADMET: Toxicity

hERG Blockers:  0.435
Human Hepatotoxicity (H-HT):  0.82
Drug-inuced Liver Injury (DILI):  0.792
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.286
Maximum Recommended Daily Dose:  0.862
Skin Sensitization:  0.744
Carcinogencity:  0.153
Eye Corrosion:  0.005
Eye Irritation:  0.016
Respiratory Toxicity:  0.173

Download Data

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

  Natural Product: NPC67118

Natural Product ID:  NPC67118
Common Name*:   PYMYPHUHKUWMLA-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PYMYPHUHKUWMLA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2
SMILES:  C(=O)C(C(C(CO)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   854
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001540] Monosaccharides
            • [CHEMONTID:0001497] Pentoses

*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
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. DOI[10.1002/ejlt.201100207]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. DOI[10.5219/332]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. PMID[24417583]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[26434122]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. n.a. PMID[26923696]
NPO28159 Rubia akane Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[8176404]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seed Oil n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28159 Rubia akane Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28159 Rubia akane Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8321 Allium chinense Species Amaryllidaceae 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
NPO25114 NPC67118 Other Seed 449.35 401 497.7 mg/100g Database [DUKE]

☑ 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 NPC67118 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 NPC67118 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