Structure

Physi-Chem Properties

Molecular Weight:  196.07
Volume:  191.655
LogP:  1.0
LogD:  0.907
LogS:  -1.508
# Rotatable Bonds:  0
TPSA:  55.9
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.42
Synthetic Accessibility Score:  4.48
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.682
MDCK Permeability:  3.597755858208984e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.472
30% Bioavailability (F30%):  0.974

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.993
Plasma Protein Binding (PPB):  58.95183563232422%
Volume Distribution (VD):  0.788
Pgp-substrate:  47.55508041381836%

ADMET: Metabolism

CYP1A2-inhibitor:  0.29
CYP1A2-substrate:  0.115
CYP2C19-inhibitor:  0.155
CYP2C19-substrate:  0.585
CYP2C9-inhibitor:  0.035
CYP2C9-substrate:  0.214
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.382
CYP3A4-inhibitor:  0.041
CYP3A4-substrate:  0.241

ADMET: Excretion

Clearance (CL):  11.486
Half-life (T1/2):  0.878

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.433
Drug-inuced Liver Injury (DILI):  0.246
AMES Toxicity:  0.152
Rat Oral Acute Toxicity:  0.898
Maximum Recommended Daily Dose:  0.863
Skin Sensitization:  0.878
Carcinogencity:  0.845
Eye Corrosion:  0.18
Eye Irritation:  0.308
Respiratory Toxicity:  0.897

Download Data

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

  Natural Product: NPC470808

Natural Product ID:  NPC470808
Common Name*:   Stagonolide H
IUPAC Name:   (1S,2E,4S,5Z,9S,10R)-4-hydroxy-9-methyl-8,11-dioxabicyclo[8.1.0]undeca-2,5-dien-7-one
Synonyms:  
Standard InCHIKey:  LTZSTGONUVZIKC-KAYOFAASSA-N
Standard InCHI:  InChI=1S/C10H12O4/c1-6-10-8(14-10)4-2-7(11)3-5-9(12)13-6/h2-8,10-11H,1H3/b4-2+,5-3-/t6-,7-,8-,10+/m0/s1
SMILES:  O=C1/C=C[C@@H](O)/C=C/[C@H]2[C@@H]([C@@H](O1)C)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2251287
PubChem CID:   25156435
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0001238] Carboxylic acid esters
            • [CHEMONTID:0003628] Alpha,beta-unsaturated carboxylic esters
              • [CHEMONTID:0003626] Enoate esters

*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
NPO33443 Stagonospora cirsii Species Massarinaceae Eukaryota n.a. n.a. n.a. PMID[18088096]
NPO33443 Stagonospora cirsii Species Massarinaceae Eukaryota n.a. n.a. n.a. PMID[18959441]

☑ 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
NPT120 Organism Zea mays Zea mays Activity < 4.0 mm PMID[568635]
NPT6543 Organism Elymus repens Elymus repens Activity < 4.0 mm PMID[568635]
NPT959 Organism Solanum lycopersicum Solanum lycopersicum Activity < 4.0 mm PMID[568635]
NPT527 Organism Radish Raphanus sativus Activity < 4.0 mm PMID[568635]
NPT594 Organism Trifolium pratense Trifolium pratense Activity < 4.0 mm PMID[568635]
NPT6354 Organism Aegopodium podagraria Aegopodium podagraria Activity < 4.0 mm PMID[568635]
NPT6414 Organism Cichorium intybus Cichorium intybus Activity < 4.0 mm PMID[568635]
NPT2537 Organism Cirsium arvense Cirsium arvense Activity = 7.5 mm PMID[568635]
NPT6414 Organism Cichorium intybus Cichorium intybus GI = 85.0 % PMID[568635]
NPT2537 Organism Cirsium arvense Cirsium arvense MIC = 150000.0 nM PMID[568635]

☑ 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 NPC470808 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
0.9 High Similarity NPC97570
0.8485 Intermediate Similarity NPC63873
0.8308 Intermediate Similarity NPC96414
0.8308 Intermediate Similarity NPC19769
0.8194 Intermediate Similarity NPC318481
0.8182 Intermediate Similarity NPC201356
0.8182 Intermediate Similarity NPC276299
0.8154 Intermediate Similarity NPC308457
0.8095 Intermediate Similarity NPC302564
0.791 Intermediate Similarity NPC124586
0.791 Intermediate Similarity NPC146811
0.7887 Intermediate Similarity NPC326504
0.7846 Intermediate Similarity NPC26810
0.7826 Intermediate Similarity NPC475982
0.7778 Intermediate Similarity NPC473582
0.7761 Intermediate Similarity NPC273600
0.7761 Intermediate Similarity NPC470123
0.7727 Intermediate Similarity NPC473737
0.7692 Intermediate Similarity NPC26223
0.7639 Intermediate Similarity NPC473489
0.7612 Intermediate Similarity NPC25747
0.7612 Intermediate Similarity NPC148233
0.7536 Intermediate Similarity NPC122627
0.7536 Intermediate Similarity NPC25298
0.75 Intermediate Similarity NPC129150
0.75 Intermediate Similarity NPC282760
0.7465 Intermediate Similarity NPC202011
0.7465 Intermediate Similarity NPC476037
0.7432 Intermediate Similarity NPC188860
0.7397 Intermediate Similarity NPC315843
0.7397 Intermediate Similarity NPC107654
0.7391 Intermediate Similarity NPC475675
0.7391 Intermediate Similarity NPC475555
0.7385 Intermediate Similarity NPC223679
0.7361 Intermediate Similarity NPC316185
0.7361 Intermediate Similarity NPC293114
0.7333 Intermediate Similarity NPC233071
0.7324 Intermediate Similarity NPC130618
0.7313 Intermediate Similarity NPC55376
0.7297 Intermediate Similarity NPC161038
0.726 Intermediate Similarity NPC329890
0.726 Intermediate Similarity NPC284006
0.7246 Intermediate Similarity NPC478098
0.7246 Intermediate Similarity NPC478099
0.7237 Intermediate Similarity NPC248775
0.7231 Intermediate Similarity NPC294938
0.7231 Intermediate Similarity NPC135863
0.7222 Intermediate Similarity NPC476012
0.7213 Intermediate Similarity NPC275316
0.72 Intermediate Similarity NPC203277
0.7183 Intermediate Similarity NPC475760
0.7143 Intermediate Similarity NPC470149
0.7143 Intermediate Similarity NPC180725
0.7143 Intermediate Similarity NPC478101
0.7143 Intermediate Similarity NPC37382
0.7143 Intermediate Similarity NPC1180
0.7143 Intermediate Similarity NPC470148
0.7121 Intermediate Similarity NPC254095
0.7105 Intermediate Similarity NPC275530
0.7105 Intermediate Similarity NPC474026
0.7101 Intermediate Similarity NPC475221
0.7083 Intermediate Similarity NPC151481
0.7077 Intermediate Similarity NPC324224
0.7077 Intermediate Similarity NPC472808
0.7077 Intermediate Similarity NPC230296
0.7059 Intermediate Similarity NPC113293
0.7051 Intermediate Similarity NPC133226
0.7051 Intermediate Similarity NPC470147
0.7042 Intermediate Similarity NPC478100
0.7042 Intermediate Similarity NPC478097
0.7027 Intermediate Similarity NPC329914
0.7027 Intermediate Similarity NPC185186
0.7027 Intermediate Similarity NPC327383
0.7015 Intermediate Similarity NPC159650
0.7015 Intermediate Similarity NPC82465
0.7015 Intermediate Similarity NPC22897
0.7013 Intermediate Similarity NPC473471
0.7013 Intermediate Similarity NPC279532
0.6974 Remote Similarity NPC209113
0.6974 Remote Similarity NPC301207
0.6974 Remote Similarity NPC127118
0.697 Remote Similarity NPC249850
0.697 Remote Similarity NPC212730
0.697 Remote Similarity NPC265551
0.697 Remote Similarity NPC293437
0.6957 Remote Similarity NPC475073
0.6944 Remote Similarity NPC238223
0.6933 Remote Similarity NPC474280
0.6933 Remote Similarity NPC474545
0.6933 Remote Similarity NPC114727
0.6933 Remote Similarity NPC476590
0.6914 Remote Similarity NPC78673
0.6914 Remote Similarity NPC160517
0.6914 Remote Similarity NPC186155
0.6912 Remote Similarity NPC258788
0.6912 Remote Similarity NPC98519
0.6912 Remote Similarity NPC130953
0.6892 Remote Similarity NPC475762
0.6883 Remote Similarity NPC49302
0.6883 Remote Similarity NPC51809
0.6883 Remote Similarity NPC176329
0.6883 Remote Similarity NPC474818
0.6883 Remote Similarity NPC125365
0.6883 Remote Similarity NPC475711
0.6866 Remote Similarity NPC474084
0.6866 Remote Similarity NPC478096
0.6866 Remote Similarity NPC187770
0.6866 Remote Similarity NPC21946
0.6842 Remote Similarity NPC478196
0.6842 Remote Similarity NPC327041
0.6842 Remote Similarity NPC478192
0.6842 Remote Similarity NPC478195
0.6842 Remote Similarity NPC478191
0.6842 Remote Similarity NPC478193
0.6842 Remote Similarity NPC478194
0.6842 Remote Similarity NPC285840
0.6842 Remote Similarity NPC260396
0.6835 Remote Similarity NPC121374
0.6806 Remote Similarity NPC132286
0.68 Remote Similarity NPC470435
0.6795 Remote Similarity NPC221095
0.6795 Remote Similarity NPC279214
0.6795 Remote Similarity NPC28049
0.679 Remote Similarity NPC315559
0.679 Remote Similarity NPC44261
0.679 Remote Similarity NPC473315
0.679 Remote Similarity NPC142111
0.6765 Remote Similarity NPC286189
0.6765 Remote Similarity NPC478095
0.6765 Remote Similarity NPC222852
0.6765 Remote Similarity NPC322186
0.6757 Remote Similarity NPC329904
0.6757 Remote Similarity NPC473361
0.6757 Remote Similarity NPC59558
0.6753 Remote Similarity NPC470705
0.6753 Remote Similarity NPC326661
0.6753 Remote Similarity NPC68819
0.675 Remote Similarity NPC297440
0.6747 Remote Similarity NPC61527
0.6716 Remote Similarity NPC44542
0.6716 Remote Similarity NPC319423
0.6716 Remote Similarity NPC472445
0.6714 Remote Similarity NPC68110
0.6714 Remote Similarity NPC474774
0.6714 Remote Similarity NPC2328
0.6712 Remote Similarity NPC474823
0.6709 Remote Similarity NPC99651
0.6709 Remote Similarity NPC471537
0.6707 Remote Similarity NPC473308
0.6667 Remote Similarity NPC474278
0.6667 Remote Similarity NPC474913
0.6667 Remote Similarity NPC81896
0.6667 Remote Similarity NPC310450
0.6667 Remote Similarity NPC251026
0.6667 Remote Similarity NPC475046
0.6667 Remote Similarity NPC11383
0.6667 Remote Similarity NPC471278
0.6667 Remote Similarity NPC321919
0.6667 Remote Similarity NPC313677
0.6667 Remote Similarity NPC236338
0.6667 Remote Similarity NPC15789
0.6667 Remote Similarity NPC474959
0.6628 Remote Similarity NPC3952
0.6623 Remote Similarity NPC473948
0.6622 Remote Similarity NPC470436
0.6622 Remote Similarity NPC475004
0.6618 Remote Similarity NPC189700
0.6615 Remote Similarity NPC477780
0.6615 Remote Similarity NPC477781
0.661 Remote Similarity NPC57923
0.661 Remote Similarity NPC41409
0.6588 Remote Similarity NPC287089
0.6585 Remote Similarity NPC286770
0.6585 Remote Similarity NPC284472
0.6585 Remote Similarity NPC229799
0.6585 Remote Similarity NPC161045
0.6571 Remote Similarity NPC325929
0.6571 Remote Similarity NPC151648
0.6571 Remote Similarity NPC263732
0.6571 Remote Similarity NPC66460
0.6571 Remote Similarity NPC15193
0.6571 Remote Similarity NPC271282
0.6567 Remote Similarity NPC245002
0.6567 Remote Similarity NPC327388
0.6548 Remote Similarity NPC208473
0.6543 Remote Similarity NPC150502
0.6543 Remote Similarity NPC469469
0.6543 Remote Similarity NPC315731
0.6528 Remote Similarity NPC476589
0.6522 Remote Similarity NPC318306
0.6515 Remote Similarity NPC159535
0.6515 Remote Similarity NPC151761
0.6512 Remote Similarity NPC83423
0.6506 Remote Similarity NPC475035
0.6506 Remote Similarity NPC161670
0.65 Remote Similarity NPC475210
0.65 Remote Similarity NPC139712
0.6494 Remote Similarity NPC470686
0.6486 Remote Similarity NPC310210
0.6479 Remote Similarity NPC210303

  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 NPC470808 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
0.7656 Intermediate Similarity NPD585 Clinical (unspecified phase)
0.6866 Remote Similarity NPD9119 Approved
0.6866 Remote Similarity NPD69 Approved
0.6716 Remote Similarity NPD9118 Approved
0.6437 Remote Similarity NPD7838 Discovery
0.6301 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6143 Remote Similarity NPD6109 Phase 1
0.6067 Remote Similarity NPD6698 Approved
0.6067 Remote Similarity NPD46 Approved
0.6061 Remote Similarity NPD6927 Phase 3
0.6 Remote Similarity NPD4220 Pre-registration
0.6 Remote Similarity NPD5344 Discontinued
0.5972 Remote Similarity NPD4246 Clinical (unspecified phase)
0.593 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5921 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5895 Remote Similarity NPD6648 Approved
0.5763 Remote Similarity NPD9115 Approved
0.5682 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5647 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6096 Approved
0.5625 Remote Similarity NPD4225 Approved
0.5625 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6097 Approved
0.5606 Remote Similarity NPD5343 Approved

  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