Structure

Physi-Chem Properties

Molecular Weight:  452.29
Volume:  513.016
LogP:  6.679
LogD:  4.97
LogS:  -4.32
# Rotatable Bonds:  13
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.147
Synthetic Accessibility Score:  3.391
Fsp3:  0.414
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.986
MDCK Permeability:  2.9881004593335092e-05
Pgp-inhibitor:  0.967
Pgp-substrate:  0.072
Human Intestinal Absorption (HIA):  0.699
20% Bioavailability (F20%):  0.982
30% Bioavailability (F30%):  0.872

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.098
Plasma Protein Binding (PPB):  99.24102020263672%
Volume Distribution (VD):  5.365
Pgp-substrate:  0.6163461804389954%

ADMET: Metabolism

CYP1A2-inhibitor:  0.771
CYP1A2-substrate:  0.354
CYP2C19-inhibitor:  0.48
CYP2C19-substrate:  0.236
CYP2C9-inhibitor:  0.575
CYP2C9-substrate:  0.965
CYP2D6-inhibitor:  0.932
CYP2D6-substrate:  0.921
CYP3A4-inhibitor:  0.839
CYP3A4-substrate:  0.268

ADMET: Excretion

Clearance (CL):  6.268
Half-life (T1/2):  0.918

ADMET: Toxicity

hERG Blockers:  0.583
Human Hepatotoxicity (H-HT):  0.958
Drug-inuced Liver Injury (DILI):  0.024
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.944
Skin Sensitization:  0.956
Carcinogencity:  0.189
Eye Corrosion:  0.003
Eye Irritation:  0.504
Respiratory Toxicity:  0.782

Download Data

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

  Natural Product: NPC79756

Natural Product ID:  NPC79756
Common Name*:   Chabrolobenzoquinone F
IUPAC Name:   [(2Z,6E,10E)-6,10-dimethyl-12-(4-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)-2-(4-methylpent-3-enyl)dodeca-2,6,10-trienyl] acetate
Synonyms:   Chabrolobenzoquinone F
Standard InCHIKey:  KAWZUHAIGPPTAK-LTZIXBDESA-N
Standard InCHI:  InChI=1S/C29H40O4/c1-21(2)10-7-14-26(20-33-25(6)30)15-9-13-22(3)11-8-12-23(4)16-17-27-19-28(31)24(5)18-29(27)32/h10-11,15-16,18-19H,7-9,12-14,17,20H2,1-6H3/b22-11+,23-16+,26-15-
SMILES:  CC(=O)OC/C(=CCC/C(=C/CC/C(=C/CC1=CC(=O)C(=CC1=O)C)/C)/C)/CCC=C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464943
PubChem CID:   5326353
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. Formosan soft coral n.a. PMID[16309317]
NPO16934 Nephthea chabrolii Species Nephtheidae 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
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 = 33200.0 nM PMID[514809]
NPT65 Cell Line HepG2 Homo sapiens IC50 = 38100.0 nM PMID[514809]
NPT81 Cell Line A549 Homo sapiens IC50 = 38100.0 nM PMID[514809]

☑ 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 NPC79756 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
0.9032 High Similarity NPC203335
0.8525 High Similarity NPC151648
0.8214 Intermediate Similarity NPC236338
0.8167 Intermediate Similarity NPC249850
0.8167 Intermediate Similarity NPC293437
0.8095 Intermediate Similarity NPC68110
0.8036 Intermediate Similarity NPC135698
0.8033 Intermediate Similarity NPC254095
0.8033 Intermediate Similarity NPC21946
0.8 Intermediate Similarity NPC248125
0.791 Intermediate Similarity NPC88877
0.791 Intermediate Similarity NPC476591
0.7903 Intermediate Similarity NPC82465
0.7869 Intermediate Similarity NPC129150
0.7869 Intermediate Similarity NPC283502
0.7869 Intermediate Similarity NPC268185
0.7869 Intermediate Similarity NPC294938
0.7869 Intermediate Similarity NPC135863
0.7812 Intermediate Similarity NPC474658
0.7778 Intermediate Similarity NPC26223
0.7761 Intermediate Similarity NPC470256
0.7746 Intermediate Similarity NPC27205
0.7742 Intermediate Similarity NPC223679
0.7681 Intermediate Similarity NPC257618
0.7681 Intermediate Similarity NPC84038
0.7679 Intermediate Similarity NPC197467
0.7679 Intermediate Similarity NPC128280
0.7612 Intermediate Similarity NPC194871
0.7586 Intermediate Similarity NPC15789
0.7576 Intermediate Similarity NPC282760
0.7576 Intermediate Similarity NPC182794
0.7576 Intermediate Similarity NPC470688
0.7571 Intermediate Similarity NPC474705
0.7571 Intermediate Similarity NPC287878
0.7541 Intermediate Similarity NPC173157
0.7538 Intermediate Similarity NPC474774
0.7538 Intermediate Similarity NPC155849
0.7536 Intermediate Similarity NPC469660
0.75 Intermediate Similarity NPC218477
0.75 Intermediate Similarity NPC47946
0.75 Intermediate Similarity NPC26600
0.75 Intermediate Similarity NPC270706
0.7465 Intermediate Similarity NPC15499
0.7465 Intermediate Similarity NPC117746
0.7465 Intermediate Similarity NPC474758
0.7465 Intermediate Similarity NPC294434
0.7465 Intermediate Similarity NPC259599
0.7432 Intermediate Similarity NPC471299
0.7424 Intermediate Similarity NPC148233
0.7424 Intermediate Similarity NPC308457
0.7424 Intermediate Similarity NPC25747
0.7419 Intermediate Similarity NPC221763
0.7419 Intermediate Similarity NPC150717
0.7391 Intermediate Similarity NPC151481
0.7385 Intermediate Similarity NPC26810
0.7344 Intermediate Similarity NPC159650
0.7344 Intermediate Similarity NPC133600
0.7344 Intermediate Similarity NPC22897
0.7344 Intermediate Similarity NPC286189
0.7324 Intermediate Similarity NPC16349
0.7324 Intermediate Similarity NPC222244
0.7321 Intermediate Similarity NPC477686
0.7302 Intermediate Similarity NPC200831
0.7302 Intermediate Similarity NPC299369
0.7302 Intermediate Similarity NPC224103
0.7286 Intermediate Similarity NPC202011
0.7273 Intermediate Similarity NPC44343
0.7273 Intermediate Similarity NPC179087
0.7273 Intermediate Similarity NPC210303
0.7273 Intermediate Similarity NPC2328
0.7273 Intermediate Similarity NPC217940
0.726 Intermediate Similarity NPC256640
0.726 Intermediate Similarity NPC16279
0.726 Intermediate Similarity NPC205615
0.7237 Intermediate Similarity NPC275507
0.7231 Intermediate Similarity NPC19241
0.7231 Intermediate Similarity NPC143857
0.7231 Intermediate Similarity NPC309408
0.7231 Intermediate Similarity NPC229252
0.7222 Intermediate Similarity NPC114727
0.7222 Intermediate Similarity NPC476355
0.7222 Intermediate Similarity NPC160540
0.7222 Intermediate Similarity NPC476590
0.7222 Intermediate Similarity NPC140287
0.7206 Intermediate Similarity NPC475555
0.7206 Intermediate Similarity NPC146811
0.7206 Intermediate Similarity NPC475675
0.7206 Intermediate Similarity NPC124586
0.7193 Intermediate Similarity NPC191337
0.7188 Intermediate Similarity NPC478096
0.7183 Intermediate Similarity NPC186531
0.7183 Intermediate Similarity NPC316185
0.7164 Intermediate Similarity NPC34883
0.7162 Intermediate Similarity NPC57744
0.7143 Intermediate Similarity NPC470693
0.7143 Intermediate Similarity NPC476059
0.7143 Intermediate Similarity NPC473603
0.7143 Intermediate Similarity NPC475982
0.7123 Intermediate Similarity NPC244166
0.7123 Intermediate Similarity NPC329826
0.7123 Intermediate Similarity NPC260396
0.7123 Intermediate Similarity NPC469414
0.7121 Intermediate Similarity NPC263732
0.7121 Intermediate Similarity NPC15193
0.7101 Intermediate Similarity NPC472266
0.7101 Intermediate Similarity NPC122627
0.7097 Intermediate Similarity NPC317796
0.7097 Intermediate Similarity NPC478120
0.7083 Intermediate Similarity NPC284006
0.7083 Intermediate Similarity NPC276336
0.7077 Intermediate Similarity NPC478095
0.7067 Intermediate Similarity NPC128276
0.7067 Intermediate Similarity NPC471220
0.7059 Intermediate Similarity NPC471565
0.7059 Intermediate Similarity NPC131174
0.7059 Intermediate Similarity NPC133904
0.7059 Intermediate Similarity NPC96414
0.7059 Intermediate Similarity NPC471556
0.7059 Intermediate Similarity NPC273600
0.7059 Intermediate Similarity NPC471566
0.7051 Intermediate Similarity NPC16488
0.7049 Intermediate Similarity NPC151919
0.7049 Intermediate Similarity NPC191643
0.7027 Intermediate Similarity NPC203277
0.7027 Intermediate Similarity NPC123360
0.7015 Intermediate Similarity NPC473737
0.7013 Intermediate Similarity NPC471325
0.7 Intermediate Similarity NPC134385
0.7 Intermediate Similarity NPC275316
0.7 Intermediate Similarity NPC27264
0.7 Intermediate Similarity NPC287705
0.7 Intermediate Similarity NPC475760
0.7 Intermediate Similarity NPC276290
0.6986 Remote Similarity NPC315843
0.6986 Remote Similarity NPC107654
0.6984 Remote Similarity NPC474913
0.6974 Remote Similarity NPC270126
0.6974 Remote Similarity NPC178277
0.6962 Remote Similarity NPC474865
0.6962 Remote Similarity NPC163615
0.6962 Remote Similarity NPC31086
0.6962 Remote Similarity NPC38569
0.6957 Remote Similarity NPC284447
0.6957 Remote Similarity NPC201356
0.6957 Remote Similarity NPC478101
0.6944 Remote Similarity NPC133098
0.6944 Remote Similarity NPC163003
0.6944 Remote Similarity NPC293114
0.6935 Remote Similarity NPC474805
0.6933 Remote Similarity NPC10572
0.6933 Remote Similarity NPC97516
0.6933 Remote Similarity NPC187568
0.6933 Remote Similarity NPC473825
0.6933 Remote Similarity NPC68156
0.6933 Remote Similarity NPC41780
0.6933 Remote Similarity NPC471225
0.6923 Remote Similarity NPC10080
0.6923 Remote Similarity NPC123908
0.6901 Remote Similarity NPC265574
0.6892 Remote Similarity NPC478192
0.6892 Remote Similarity NPC329852
0.6892 Remote Similarity NPC478195
0.6892 Remote Similarity NPC478196
0.6892 Remote Similarity NPC478193
0.6892 Remote Similarity NPC478194
0.6892 Remote Similarity NPC478191
0.6885 Remote Similarity NPC148056
0.6875 Remote Similarity NPC245002
0.6875 Remote Similarity NPC471300
0.6875 Remote Similarity NPC474860
0.6875 Remote Similarity NPC86948
0.6875 Remote Similarity NPC96663
0.6875 Remote Similarity NPC189311
0.6875 Remote Similarity NPC155873
0.6866 Remote Similarity NPC55376
0.6857 Remote Similarity NPC478100
0.6857 Remote Similarity NPC225272
0.6857 Remote Similarity NPC478097
0.6857 Remote Similarity NPC132286
0.6857 Remote Similarity NPC21998
0.6849 Remote Similarity NPC185186
0.6849 Remote Similarity NPC327383
0.6849 Remote Similarity NPC476489
0.6849 Remote Similarity NPC476490
0.6842 Remote Similarity NPC182292
0.6842 Remote Similarity NPC209135
0.6842 Remote Similarity NPC474816
0.6842 Remote Similarity NPC279532
0.6842 Remote Similarity NPC477314
0.6842 Remote Similarity NPC108816
0.6842 Remote Similarity NPC93763
0.6835 Remote Similarity NPC144415
0.6833 Remote Similarity NPC15912
0.6825 Remote Similarity NPC159535
0.6825 Remote Similarity NPC151761
0.6818 Remote Similarity NPC97570
0.6818 Remote Similarity NPC474267
0.6818 Remote Similarity NPC86789
0.6812 Remote Similarity NPC220766
0.6812 Remote Similarity NPC19769

  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 NPC79756 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
0.8393 Intermediate Similarity NPD6927 Phase 3
0.7302 Intermediate Similarity NPD8779 Phase 3
0.7241 Intermediate Similarity NPD5343 Approved
0.7059 Intermediate Similarity NPD2685 Clinical (unspecified phase)
0.7018 Intermediate Similarity NPD6097 Approved
0.7018 Intermediate Similarity NPD6096 Approved
0.6711 Remote Similarity NPD4756 Discovery
0.6709 Remote Similarity NPD5209 Approved
0.6667 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8039 Approved
0.65 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6479 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6447 Remote Similarity NPD1452 Discontinued
0.6429 Remote Similarity NPD5783 Phase 3
0.6418 Remote Similarity NPD6109 Phase 1
0.6341 Remote Similarity NPD6400 Clinical (unspecified phase)
0.629 Remote Similarity NPD4220 Pre-registration
0.6265 Remote Similarity NPD1694 Approved
0.6232 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6092 Remote Similarity NPD6698 Approved
0.6092 Remote Similarity NPD46 Approved
0.6066 Remote Similarity NPD4222 Approved
0.6066 Remote Similarity NPD4265 Approved
0.6066 Remote Similarity NPD39 Approved
0.6066 Remote Similarity NPD3174 Discontinued
0.6056 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6 Remote Similarity NPD5326 Phase 3
0.6 Remote Similarity NPD9411 Phase 1
0.5946 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5938 Remote Similarity NPD2268 Discontinued
0.5915 Remote Similarity NPD9418 Clinical (unspecified phase)
0.5909 Remote Similarity NPD7838 Discovery
0.5909 Remote Similarity NPD5785 Approved
0.5882 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5862 Remote Similarity NPD6672 Approved
0.5862 Remote Similarity NPD5737 Approved
0.5846 Remote Similarity NPD28 Approved
0.5846 Remote Similarity NPD29 Approved
0.5833 Remote Similarity NPD6110 Phase 1
0.5814 Remote Similarity NPD7146 Approved
0.5814 Remote Similarity NPD6684 Approved
0.5814 Remote Similarity NPD5330 Approved
0.5814 Remote Similarity NPD7521 Approved
0.5814 Remote Similarity NPD7334 Approved
0.5814 Remote Similarity NPD6409 Approved
0.5811 Remote Similarity NPD3704 Approved
0.5811 Remote Similarity NPD7331 Phase 2
0.5806 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5789 Remote Similarity NPD9115 Approved
0.5781 Remote Similarity NPD3173 Approved
0.5735 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5698 Remote Similarity NPD5363 Approved
0.5694 Remote Similarity NPD4192 Approved
0.5694 Remote Similarity NPD4193 Approved
0.5694 Remote Similarity NPD4194 Approved
0.5694 Remote Similarity NPD3205 Discontinued
0.5694 Remote Similarity NPD4191 Approved
0.5682 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5682 Remote Similarity NPD6903 Approved
0.5667 Remote Similarity NPD5693 Phase 1
0.5663 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5647 Remote Similarity NPD7154 Phase 3
0.5638 Remote Similarity NPD7638 Approved
0.5638 Remote Similarity NPD4225 Approved
0.5618 Remote Similarity NPD6051 Approved
0.561 Remote Similarity NPD5784 Clinical (unspecified phase)

  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