Structure

Physi-Chem Properties

Molecular Weight:  254.15
Volume:  269.395
LogP:  0.862
LogD:  1.03
LogS:  -1.057
# Rotatable Bonds:  6
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.68
Synthetic Accessibility Score:  4.402
Fsp3:  0.714
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.658
MDCK Permeability:  3.93196169170551e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.198
Plasma Protein Binding (PPB):  80.71540069580078%
Volume Distribution (VD):  1.296
Pgp-substrate:  25.250932693481445%

ADMET: Metabolism

CYP1A2-inhibitor:  0.03
CYP1A2-substrate:  0.638
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.785
CYP2C9-inhibitor:  0.029
CYP2C9-substrate:  0.048
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.194
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.386

ADMET: Excretion

Clearance (CL):  6.524
Half-life (T1/2):  0.81

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.404
Drug-inuced Liver Injury (DILI):  0.787
AMES Toxicity:  0.146
Rat Oral Acute Toxicity:  0.283
Maximum Recommended Daily Dose:  0.138
Skin Sensitization:  0.817
Carcinogencity:  0.332
Eye Corrosion:  0.98
Eye Irritation:  0.946
Respiratory Toxicity:  0.969

Download Data

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

  Natural Product: NPC220894

Natural Product ID:  NPC220894
Common Name*:   (-)-2-Epi-Botryodiplodinenone
IUPAC Name:   (4R)-5-[(2R,3R,4S)-4-acetyl-3-methyloxolan-2-yl]oxy-4-methyl-3-methylidenepentan-2-one
Synonyms:  
Standard InCHIKey:  GHCKVZSVLOKTII-OUJOLJPFSA-N
Standard InCHI:  InChI=1S/C14H22O4/c1-8(9(2)11(4)15)6-17-14-10(3)13(7-18-14)12(5)16/h8,10,13-14H,2,6-7H2,1,3-5H3/t8-,10+,13+,14+/m0/s1
SMILES:  C[C@@H](CO[C@H]1[C@H](C)[C@@H](CO1)C(=O)C)C(=C)C(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2251622
PubChem CID:   23583010
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0003131] Alpha,beta-unsaturated carbonyl compounds
            • [CHEMONTID:0003672] Alpha,beta-unsaturated ketones
              • [CHEMONTID:0003674] Alpha-branched alpha,beta-unsaturated ketones

*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
NPO15176 Centaurea deflexa Species Asteraceae Eukaryota aerial parts n.a. n.a. PMID[21458113]
NPO7413 Wedelia biflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15678 Scarites subterraneus Species Carabidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16622 Cathartus quadricollis Species Silvanidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15176 Centaurea deflexa Species Asteraceae 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
NPT2212 Organism Oncopeltus fasciatus Oncopeltus fasciatus LD50 > 15.0 ug PMID[464185]

☑ 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 NPC220894 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
0.7966 Intermediate Similarity NPC233143
0.7419 Intermediate Similarity NPC216382
0.6667 Remote Similarity NPC474658
0.6575 Remote Similarity NPC476591
0.6575 Remote Similarity NPC88877
0.6447 Remote Similarity NPC48641
0.6301 Remote Similarity NPC194871
0.625 Remote Similarity NPC19841
0.6234 Remote Similarity NPC114727
0.6234 Remote Similarity NPC476590
0.6216 Remote Similarity NPC470256
0.618 Remote Similarity NPC41649
0.6173 Remote Similarity NPC223904
0.6173 Remote Similarity NPC6823
0.6145 Remote Similarity NPC469
0.6133 Remote Similarity NPC476059
0.6133 Remote Similarity NPC473603
0.6125 Remote Similarity NPC469510
0.6118 Remote Similarity NPC238593
0.6071 Remote Similarity NPC41856
0.6053 Remote Similarity NPC472955
0.6049 Remote Similarity NPC270126
0.6026 Remote Similarity NPC140287
0.6026 Remote Similarity NPC15499
0.6026 Remote Similarity NPC259599
0.6026 Remote Similarity NPC117746
0.6026 Remote Similarity NPC476355
0.6026 Remote Similarity NPC294434
0.6 Remote Similarity NPC476028
0.6 Remote Similarity NPC300985
0.6 Remote Similarity NPC141789
0.6 Remote Similarity NPC171204
0.6 Remote Similarity NPC97516
0.5974 Remote Similarity NPC163003
0.5955 Remote Similarity NPC65513
0.5955 Remote Similarity NPC9447
0.5952 Remote Similarity NPC318468
0.5952 Remote Similarity NPC54468
0.5949 Remote Similarity NPC155587
0.5949 Remote Similarity NPC193351
0.5949 Remote Similarity NPC138408
0.5949 Remote Similarity NPC226669
0.5934 Remote Similarity NPC167893
0.593 Remote Similarity NPC304558
0.5921 Remote Similarity NPC144511
0.5921 Remote Similarity NPC5714
0.5921 Remote Similarity NPC296522
0.5909 Remote Similarity NPC12872
0.5909 Remote Similarity NPC168679
0.5909 Remote Similarity NPC170167
0.5904 Remote Similarity NPC281949
0.5904 Remote Similarity NPC149237
0.5904 Remote Similarity NPC25684
0.5904 Remote Similarity NPC39411
0.5904 Remote Similarity NPC255580
0.5904 Remote Similarity NPC301477
0.5897 Remote Similarity NPC269206
0.5897 Remote Similarity NPC287878
0.5897 Remote Similarity NPC58956
0.5897 Remote Similarity NPC472956
0.5897 Remote Similarity NPC295633
0.5882 Remote Similarity NPC32565
0.5882 Remote Similarity NPC158756
0.5882 Remote Similarity NPC120726
0.5875 Remote Similarity NPC68819
0.5875 Remote Similarity NPC123360
0.5875 Remote Similarity NPC266159
0.5875 Remote Similarity NPC472967
0.5862 Remote Similarity NPC201658
0.5862 Remote Similarity NPC265580
0.5854 Remote Similarity NPC178277
0.5854 Remote Similarity NPC323472
0.5833 Remote Similarity NPC474959
0.5833 Remote Similarity NPC310450
0.5833 Remote Similarity NPC11383
0.5833 Remote Similarity NPC475046
0.5833 Remote Similarity NPC246076
0.5823 Remote Similarity NPC320537
0.5823 Remote Similarity NPC143979
0.5823 Remote Similarity NPC238146
0.5814 Remote Similarity NPC470755
0.5814 Remote Similarity NPC21471
0.5814 Remote Similarity NPC33570
0.5814 Remote Similarity NPC217394
0.5802 Remote Similarity NPC476794
0.5802 Remote Similarity NPC474760
0.5802 Remote Similarity NPC57744
0.5802 Remote Similarity NPC195785
0.5802 Remote Similarity NPC10572
0.5802 Remote Similarity NPC208223
0.5802 Remote Similarity NPC122847
0.5802 Remote Similarity NPC15975
0.5802 Remote Similarity NPC65603
0.5802 Remote Similarity NPC470240
0.5797 Remote Similarity NPC252860
0.5795 Remote Similarity NPC137368
0.5795 Remote Similarity NPC476803
0.5795 Remote Similarity NPC476805
0.5783 Remote Similarity NPC290508
0.5783 Remote Similarity NPC69271
0.5783 Remote Similarity NPC281132
0.5783 Remote Similarity NPC74673
0.5783 Remote Similarity NPC473685
0.5783 Remote Similarity NPC73052
0.5783 Remote Similarity NPC293418
0.5783 Remote Similarity NPC51507
0.5778 Remote Similarity NPC123177
0.5778 Remote Similarity NPC70595
0.5778 Remote Similarity NPC191339
0.5778 Remote Similarity NPC286341
0.5778 Remote Similarity NPC74103
0.5778 Remote Similarity NPC150978
0.5765 Remote Similarity NPC229799
0.5765 Remote Similarity NPC284472
0.5765 Remote Similarity NPC286770
0.5765 Remote Similarity NPC215294
0.5765 Remote Similarity NPC128429
0.5761 Remote Similarity NPC473369
0.5758 Remote Similarity NPC244452
0.575 Remote Similarity NPC324762
0.5747 Remote Similarity NPC469910
0.5747 Remote Similarity NPC309757
0.5747 Remote Similarity NPC162071
0.5747 Remote Similarity NPC236692
0.5747 Remote Similarity NPC70422
0.5747 Remote Similarity NPC70555
0.5747 Remote Similarity NPC104961
0.5747 Remote Similarity NPC107787
0.5745 Remote Similarity NPC473154
0.5732 Remote Similarity NPC128276
0.5732 Remote Similarity NPC93763
0.5732 Remote Similarity NPC108816
0.573 Remote Similarity NPC174765
0.573 Remote Similarity NPC64913
0.573 Remote Similarity NPC242877
0.5714 Remote Similarity NPC103172
0.5714 Remote Similarity NPC275507
0.5714 Remote Similarity NPC477449
0.5714 Remote Similarity NPC475951
0.5714 Remote Similarity NPC24417
0.5714 Remote Similarity NPC477448
0.5714 Remote Similarity NPC47635
0.5714 Remote Similarity NPC471325
0.5714 Remote Similarity NPC164600
0.5714 Remote Similarity NPC141810
0.5714 Remote Similarity NPC471571
0.5714 Remote Similarity NPC153590
0.5714 Remote Similarity NPC199557
0.5699 Remote Similarity NPC256230
0.5699 Remote Similarity NPC306041
0.5699 Remote Similarity NPC73858
0.5698 Remote Similarity NPC163615
0.5698 Remote Similarity NPC476804
0.5698 Remote Similarity NPC141193
0.5698 Remote Similarity NPC38569
0.5698 Remote Similarity NPC96259
0.5698 Remote Similarity NPC165287
0.5698 Remote Similarity NPC469884
0.5698 Remote Similarity NPC115786
0.5696 Remote Similarity NPC238948
0.5696 Remote Similarity NPC12680
0.5696 Remote Similarity NPC12815
0.5696 Remote Similarity NPC215745
0.5684 Remote Similarity NPC469402
0.5682 Remote Similarity NPC475773
0.5682 Remote Similarity NPC266957
0.5682 Remote Similarity NPC118601
0.5682 Remote Similarity NPC241054
0.5679 Remote Similarity NPC235906
0.5679 Remote Similarity NPC472959
0.5679 Remote Similarity NPC266119
0.5667 Remote Similarity NPC253144
0.5667 Remote Similarity NPC117596
0.5667 Remote Similarity NPC19087
0.5667 Remote Similarity NPC80875
0.5663 Remote Similarity NPC167881
0.5663 Remote Similarity NPC63649
0.5663 Remote Similarity NPC98557
0.5663 Remote Similarity NPC473980
0.5663 Remote Similarity NPC473981
0.5663 Remote Similarity NPC164308
0.5663 Remote Similarity NPC472965
0.5663 Remote Similarity NPC99651
0.5663 Remote Similarity NPC617
0.5663 Remote Similarity NPC182550
0.5663 Remote Similarity NPC264227
0.5652 Remote Similarity NPC289004
0.5652 Remote Similarity NPC473331
0.5647 Remote Similarity NPC26624
0.5647 Remote Similarity NPC173609
0.5647 Remote Similarity NPC229825
0.5645 Remote Similarity NPC40805
0.5641 Remote Similarity NPC318766
0.5638 Remote Similarity NPC257726
0.5638 Remote Similarity NPC204054
0.5632 Remote Similarity NPC471060
0.5632 Remote Similarity NPC165162
0.5632 Remote Similarity NPC125290
0.5632 Remote Similarity NPC155873
0.5632 Remote Similarity NPC78089

  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 NPC220894 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
0.5694 Remote Similarity NPD1145 Discontinued
0.5647 Remote Similarity NPD5209 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