Structure

Physi-Chem Properties

Molecular Weight:  268.12
Volume:  244.381
LogP:  -1.53
LogD:  -0.252
LogS:  -0.908
# Rotatable Bonds:  2
TPSA:  112.13
# H-Bond Aceptor:  8
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.537
Synthetic Accessibility Score:  4.72
Fsp3:  0.636
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:  5.053389486420201e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.995
Human Intestinal Absorption (HIA):  0.07
20% Bioavailability (F20%):  0.997
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.334
Plasma Protein Binding (PPB):  12.717246055603027%
Volume Distribution (VD):  1.853
Pgp-substrate:  89.26377868652344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.053
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.524
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.297
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.148
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.114

ADMET: Excretion

Clearance (CL):  3.238
Half-life (T1/2):  0.694

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.861
Drug-inuced Liver Injury (DILI):  0.957
AMES Toxicity:  0.94
Rat Oral Acute Toxicity:  0.073
Maximum Recommended Daily Dose:  0.945
Skin Sensitization:  0.139
Carcinogencity:  0.961
Eye Corrosion:  0.003
Eye Irritation:  0.013
Respiratory Toxicity:  0.8

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

  Natural Product: NPC187488

Natural Product ID:  NPC187488
Common Name*:   FPVKHBSQESCIEP-RBXMUDONSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FPVKHBSQESCIEP-RBXMUDONSA-N
Standard InCHI:  InChI=1S/C11H16N4O4/c16-3-8-6(17)1-9(19-8)15-5-14-10-7(18)2-12-4-13-11(10)15/h4-9,16-18H,1-3H2,(H,12,13)/t6-,7-,8+,9+/m0/s1
SMILES:  C1[C@@H]([C@@H](CO)O[C@H]1n1cnc2[C@H](CN=CNc12)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001979] Imidazodiazepines

*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
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. aerial part n.a. DOI[10.1002/hlca.201300170.]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO17888 Myxococcus xanthus Species Myxococcaceae Bacteria n.a. n.a. n.a. PMID[12141877]
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[12735688]
NPO17888 Myxococcus xanthus Species Myxococcaceae Bacteria n.a. n.a. n.a. PMID[14575429]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota needles Himalayan n.a. PMID[16480866]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23510022]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota Stem Bark n.a. n.a. PMID[28240909]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota Roots n.a. n.a. PMID[28581744]
NPO17888 Myxococcus xanthus Species Myxococcaceae Bacteria n.a. n.a. n.a. PMID[31465225]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[7264680]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21175 Senecio retrorsus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21175 Senecio retrorsus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17801 Drimia altissima Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23431 Aconitum umbrosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20290 Vernonia arkansana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17888 Myxococcus xanthus Species Myxococcaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16976 Phebalium rotundifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21175 Senecio retrorsus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23611 Conyza pallidiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13151.1 Pulsatilla vulgaris subsp. grandis Subspecies Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6439 Lithospermum carolinense Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17801 Drimia altissima Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23981 Maytenus disticha Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26544 Bolboschoenus maritimus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24063 Evasterias retifera Species Asteriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23175 Streptomyces antibioticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO23431 Aconitum umbrosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23686 Selinum tenuifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19539 Uperoleia rugosa Species Myobatrachidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9228.2 Narcissus pseudonarcissus subsp. radinganorum Subspecies Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21915 Diospyros chloroxylon Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23781 Lemaireocereus stellatus Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23688 Lonicera nitida Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22028 Ligularia lankongensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23363 0dulisporium hinnuleum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23268 Xanthorrhoea reflexa Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23113 Garcinia neglecta Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21747 Sideritis glacialis Species Lamiaceae 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 NPC187488 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 NPC187488 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