Structure

Physi-Chem Properties

Molecular Weight:  402.13
Volume:  395.333
LogP:  2.544
LogD:  2.37
LogS:  -3.54
# Rotatable Bonds:  6
TPSA:  112.27
# H-Bond Aceptor:  8
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.595
Synthetic Accessibility Score:  5.649
Fsp3:  0.381
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.074
MDCK Permeability:  1.946999145729933e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.966
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.015
30% Bioavailability (F30%):  0.035

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.104
Plasma Protein Binding (PPB):  76.25679779052734%
Volume Distribution (VD):  1.027
Pgp-substrate:  25.645490646362305%

ADMET: Metabolism

CYP1A2-inhibitor:  0.279
CYP1A2-substrate:  0.119
CYP2C19-inhibitor:  0.075
CYP2C19-substrate:  0.225
CYP2C9-inhibitor:  0.476
CYP2C9-substrate:  0.12
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.043
CYP3A4-inhibitor:  0.386
CYP3A4-substrate:  0.648

ADMET: Excretion

Clearance (CL):  13.124
Half-life (T1/2):  0.913

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.162
Drug-inuced Liver Injury (DILI):  0.948
AMES Toxicity:  0.922
Rat Oral Acute Toxicity:  0.981
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.94
Carcinogencity:  0.639
Eye Corrosion:  0.99
Eye Irritation:  0.736
Respiratory Toxicity:  0.951

Download Data

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

  Natural Product: NPC130030

Natural Product ID:  NPC130030
Common Name*:   [(1S,2E,8S,10S)-6-(acetyloxymethyl)-1,10-dimethyl-5,13-dioxo-4,14-dioxatricyclo[9.2.1.03,7]tetradeca-2,6,11-trien-8-yl] 2-methylprop-2-enoate
IUPAC Name:   [(1S,2E,8S,10S)-6-(acetyloxymethyl)-1,10-dimethyl-5,13-dioxo-4,14-dioxatricyclo[9.2.1.03,7]tetradeca-2,6,11-trien-8-yl] 2-methylprop-2-enoate
Synonyms:  
Standard InCHIKey:  QGSLMVGRLUHZPH-YXWKBXDBSA-N
Standard InCHI:  InChI=1S/C21H22O8/c1-10(2)19(24)27-15-6-11(3)14-7-17(23)21(5,29-14)8-16-18(15)13(20(25)28-16)9-26-12(4)22/h7-8,11,15H,1,6,9H2,2-5H3/b16-8+/t11-,15-,21-/m0/s1
SMILES:  C[C@H]1C[C@@H](C\2=C(C(=O)O/C2=C/[C@]3(C(=O)C=C1O3)C)COC(=O)C)OC(=O)C(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   49799775
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001986] Tricarboxylic acids and derivatives

*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
NPO24700 Vernonia staehelinoides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[19299148]

☑ 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
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 1.8 ug/ml PMID[19299148]

☑ 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 NPC130030 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
0.8409 Intermediate Similarity NPC242877
0.8409 Intermediate Similarity NPC64913
0.8222 Intermediate Similarity NPC32494
0.8222 Intermediate Similarity NPC175842
0.8065 Intermediate Similarity NPC301596
0.8065 Intermediate Similarity NPC299396
0.7935 Intermediate Similarity NPC59646
0.7889 Intermediate Similarity NPC260343
0.7872 Intermediate Similarity NPC172998
0.7857 Intermediate Similarity NPC68156
0.7857 Intermediate Similarity NPC471225
0.7849 Intermediate Similarity NPC470521
0.7766 Intermediate Similarity NPC273197
0.7766 Intermediate Similarity NPC234339
0.7717 Intermediate Similarity NPC3436
0.7692 Intermediate Similarity NPC475902
0.7667 Intermediate Similarity NPC291712
0.7653 Intermediate Similarity NPC197835
0.7653 Intermediate Similarity NPC303653
0.7653 Intermediate Similarity NPC189609
0.7653 Intermediate Similarity NPC291500
0.7653 Intermediate Similarity NPC140591
0.7634 Intermediate Similarity NPC470520
0.7609 Intermediate Similarity NPC225283
0.7604 Intermediate Similarity NPC471490
0.7549 Intermediate Similarity NPC38154
0.75 Intermediate Similarity NPC469653
0.75 Intermediate Similarity NPC471047
0.75 Intermediate Similarity NPC469631
0.75 Intermediate Similarity NPC469628
0.75 Intermediate Similarity NPC475906
0.7439 Intermediate Similarity NPC470693
0.7396 Intermediate Similarity NPC471492
0.7263 Intermediate Similarity NPC193396
0.7263 Intermediate Similarity NPC166110
0.7263 Intermediate Similarity NPC32944
0.7245 Intermediate Similarity NPC2666
0.7234 Intermediate Similarity NPC142159
0.7234 Intermediate Similarity NPC95364
0.72 Intermediate Similarity NPC469851
0.7188 Intermediate Similarity NPC248193
0.7176 Intermediate Similarity NPC287878
0.7174 Intermediate Similarity NPC281172
0.7174 Intermediate Similarity NPC471223
0.7174 Intermediate Similarity NPC67081
0.716 Intermediate Similarity NPC220766
0.7143 Intermediate Similarity NPC473333
0.7113 Intermediate Similarity NPC469632
0.7097 Intermediate Similarity NPC38576
0.7097 Intermediate Similarity NPC204048
0.7097 Intermediate Similarity NPC279859
0.7097 Intermediate Similarity NPC261721
0.7093 Intermediate Similarity NPC474758
0.7093 Intermediate Similarity NPC470686
0.7083 Intermediate Similarity NPC32552
0.7073 Intermediate Similarity NPC248125
0.7073 Intermediate Similarity NPC191233
0.7071 Intermediate Similarity NPC471462
0.7045 Intermediate Similarity NPC473825
0.7045 Intermediate Similarity NPC10572
0.7041 Intermediate Similarity NPC12727
0.7024 Intermediate Similarity NPC232812
0.7024 Intermediate Similarity NPC476591
0.7024 Intermediate Similarity NPC88877
0.7021 Intermediate Similarity NPC266957
0.7021 Intermediate Similarity NPC471739
0.7011 Intermediate Similarity NPC329826
0.7011 Intermediate Similarity NPC469414
0.701 Intermediate Similarity NPC165383
0.697 Remote Similarity NPC17585
0.6957 Remote Similarity NPC474703
0.6947 Remote Similarity NPC471956
0.6941 Remote Similarity NPC64234
0.6941 Remote Similarity NPC37929
0.6939 Remote Similarity NPC143210
0.6932 Remote Similarity NPC123360
0.6923 Remote Similarity NPC42470
0.6923 Remote Similarity NPC469852
0.6923 Remote Similarity NPC112868
0.6907 Remote Similarity NPC20713
0.6897 Remote Similarity NPC117746
0.6897 Remote Similarity NPC294434
0.6897 Remote Similarity NPC259599
0.6897 Remote Similarity NPC15499
0.6889 Remote Similarity NPC271632
0.6889 Remote Similarity NPC270126
0.6889 Remote Similarity NPC178277
0.6863 Remote Similarity NPC46998
0.6863 Remote Similarity NPC110443
0.6863 Remote Similarity NPC133907
0.6863 Remote Similarity NPC185141
0.6863 Remote Similarity NPC128733
0.686 Remote Similarity NPC316185
0.686 Remote Similarity NPC133098
0.6857 Remote Similarity NPC469853
0.6854 Remote Similarity NPC97516
0.6832 Remote Similarity NPC54843
0.6827 Remote Similarity NPC477510
0.6827 Remote Similarity NPC471143
0.6818 Remote Similarity NPC329852
0.6804 Remote Similarity NPC475879
0.68 Remote Similarity NPC173329
0.68 Remote Similarity NPC288350
0.679 Remote Similarity NPC151648
0.6786 Remote Similarity NPC203335
0.6778 Remote Similarity NPC99182
0.6778 Remote Similarity NPC469510
0.6774 Remote Similarity NPC475947
0.6774 Remote Similarity NPC475989
0.6774 Remote Similarity NPC475714
0.6771 Remote Similarity NPC475819
0.6771 Remote Similarity NPC287089
0.6768 Remote Similarity NPC140543
0.6768 Remote Similarity NPC121825
0.6765 Remote Similarity NPC477512
0.6747 Remote Similarity NPC476589
0.6747 Remote Similarity NPC470688
0.6742 Remote Similarity NPC301525
0.6739 Remote Similarity NPC141810
0.6739 Remote Similarity NPC471325
0.6739 Remote Similarity NPC281949
0.6739 Remote Similarity NPC25684
0.6739 Remote Similarity NPC301477
0.6737 Remote Similarity NPC107787
0.6737 Remote Similarity NPC469483
0.6735 Remote Similarity NPC158061
0.6733 Remote Similarity NPC471140
0.6731 Remote Similarity NPC25666
0.6731 Remote Similarity NPC472755
0.6731 Remote Similarity NPC271059
0.6707 Remote Similarity NPC44343
0.6707 Remote Similarity NPC179087
0.6707 Remote Similarity NPC210303
0.6706 Remote Similarity NPC470256
0.6706 Remote Similarity NPC276290
0.6705 Remote Similarity NPC315843
0.6705 Remote Similarity NPC476355
0.6705 Remote Similarity NPC107654
0.6703 Remote Similarity NPC99651
0.6702 Remote Similarity NPC115786
0.6702 Remote Similarity NPC475706
0.6701 Remote Similarity NPC280833
0.6699 Remote Similarity NPC264477
0.6699 Remote Similarity NPC164598
0.6699 Remote Similarity NPC477511
0.6699 Remote Similarity NPC474339
0.6697 Remote Similarity NPC66108
0.6667 Remote Similarity NPC478144
0.6667 Remote Similarity NPC469645
0.6667 Remote Similarity NPC315115
0.6667 Remote Similarity NPC57744
0.6667 Remote Similarity NPC474439
0.6667 Remote Similarity NPC221231
0.6667 Remote Similarity NPC476028
0.6667 Remote Similarity NPC475098
0.6667 Remote Similarity NPC474028
0.6667 Remote Similarity NPC26624
0.6667 Remote Similarity NPC478145
0.6667 Remote Similarity NPC180290
0.6667 Remote Similarity NPC189651
0.6667 Remote Similarity NPC293114
0.6667 Remote Similarity NPC282644
0.6667 Remote Similarity NPC10080
0.6667 Remote Similarity NPC141789
0.6667 Remote Similarity NPC475302
0.6667 Remote Similarity NPC173609
0.6667 Remote Similarity NPC471144
0.6667 Remote Similarity NPC123908
0.6667 Remote Similarity NPC84038
0.6667 Remote Similarity NPC272528
0.6667 Remote Similarity NPC171204
0.6667 Remote Similarity NPC29798
0.6667 Remote Similarity NPC471326
0.6667 Remote Similarity NPC469692
0.6635 Remote Similarity NPC472754
0.6635 Remote Similarity NPC149371
0.6634 Remote Similarity NPC476275
0.6633 Remote Similarity NPC475995
0.6633 Remote Similarity NPC474098
0.6633 Remote Similarity NPC224270
0.6632 Remote Similarity NPC78089
0.6632 Remote Similarity NPC471185
0.6632 Remote Similarity NPC474424
0.6632 Remote Similarity NPC215364
0.6632 Remote Similarity NPC470755
0.663 Remote Similarity NPC281132
0.6629 Remote Similarity NPC478196
0.6629 Remote Similarity NPC478191
0.6629 Remote Similarity NPC478194
0.6629 Remote Similarity NPC478192
0.6629 Remote Similarity NPC478193
0.6629 Remote Similarity NPC478195
0.6628 Remote Similarity NPC265574
0.6602 Remote Similarity NPC469551
0.66 Remote Similarity NPC476596
0.66 Remote Similarity NPC476267
0.66 Remote Similarity NPC474338
0.6598 Remote Similarity NPC475739
0.6598 Remote Similarity NPC476805
0.6596 Remote Similarity NPC288281

  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 NPC130030 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
0.6848 Remote Similarity NPD5209 Approved
0.6465 Remote Similarity NPD7838 Discovery
0.6389 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6353 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6304 Remote Similarity NPD4756 Discovery
0.6214 Remote Similarity NPD1698 Clinical (unspecified phase)
0.6117 Remote Similarity NPD5282 Discontinued
0.5979 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5888 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5888 Remote Similarity NPD4225 Approved
0.5882 Remote Similarity NPD1695 Approved
0.5833 Remote Similarity NPD6648 Approved
0.5825 Remote Similarity NPD6698 Approved
0.5825 Remote Similarity NPD46 Approved
0.5825 Remote Similarity NPD5785 Approved
0.5789 Remote Similarity NPD6371 Approved
0.5789 Remote Similarity NPD2067 Discontinued
0.5769 Remote Similarity NPD7983 Approved
0.5758 Remote Similarity NPD7154 Phase 3
0.5743 Remote Similarity NPD4249 Approved
0.5714 Remote Similarity NPD8779 Phase 3
0.57 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5686 Remote Similarity NPD4250 Approved
0.5686 Remote Similarity NPD4251 Approved
0.5644 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5644 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5644 Remote Similarity NPD5363 Approved
0.5644 Remote Similarity NPD1694 Approved
0.5619 Remote Similarity NPD5693 Phase 1
0.5619 Remote Similarity NPD7637 Suspended
0.5612 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5603 Remote Similarity NPD2204 Approved
0.56 Remote Similarity NPD6110 Phase 1

  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