Structure

Physi-Chem Properties

Molecular Weight:  326.22
Volume:  379.637
LogP:  6.186
LogD:  4.589
LogS:  -4.424
# Rotatable Bonds:  7
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.343
Synthetic Accessibility Score:  3.089
Fsp3:  0.364
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:  -4.937
MDCK Permeability:  2.7348020012141205e-05
Pgp-inhibitor:  0.908
Pgp-substrate:  0.039
Human Intestinal Absorption (HIA):  0.041
20% Bioavailability (F20%):  0.988
30% Bioavailability (F30%):  0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.136
Plasma Protein Binding (PPB):  99.99278259277344%
Volume Distribution (VD):  6.518
Pgp-substrate:  0.6172773838043213%

ADMET: Metabolism

CYP1A2-inhibitor:  0.824
CYP1A2-substrate:  0.905
CYP2C19-inhibitor:  0.618
CYP2C19-substrate:  0.633
CYP2C9-inhibitor:  0.503
CYP2C9-substrate:  0.968
CYP2D6-inhibitor:  0.934
CYP2D6-substrate:  0.94
CYP3A4-inhibitor:  0.488
CYP3A4-substrate:  0.25

ADMET: Excretion

Clearance (CL):  14.926
Half-life (T1/2):  0.834

ADMET: Toxicity

hERG Blockers:  0.348
Human Hepatotoxicity (H-HT):  0.946
Drug-inuced Liver Injury (DILI):  0.009
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.056
Maximum Recommended Daily Dose:  0.895
Skin Sensitization:  0.96
Carcinogencity:  0.269
Eye Corrosion:  0.005
Eye Irritation:  0.896
Respiratory Toxicity:  0.925

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC477686

Natural Product ID:  NPC477686
Common Name*:   2-methyl-5-[(2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trienyl]cyclohexa-2,5-diene-1,4-dione
IUPAC Name:   2-methyl-5-[(2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trienyl]cyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  DMYCYVRYLFNVLN-NGEVDRGDSA-N
Standard InCHI:  InChI=1S/C22H30O2/c1-16(2)8-6-9-17(3)10-7-11-18(4)12-13-20-15-21(23)19(5)14-22(20)24/h8,10,12,14-15H,6-7,9,11,13H2,1-5H3/b17-10-,18-12-
SMILES:  CC1=CC(=O)C(=CC1=O)C/C=C(/C)\CC/C=C(/C)\CCC=C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   44566896
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
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[10479323]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12350167]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[14640527]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota Axinella verrucosa Mediterranean n.a. PMID[14738391]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15043411]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Sussex Inlet, New South Wales, Australia n.a. PMID[15104517]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15332862]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Berkeley Pit lake n.a. PMID[17970594]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. New Zealand n.a. PMID[19323568]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19326880]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20452770]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. North Sea n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Limonium tubiflorum n.a. PMID[21146414]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21916432]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22148349]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22458669]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23360521]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23477451]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23603293]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23972215]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24033077]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24437979]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[31433188]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[9392888]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[Article]

☑ 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
NPT81 Cell Line A549 Homo sapiens ED50 = 25.44 ug/ml PMID[14640527]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 = 37.29 ug/ml PMID[14640527]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 = 18.41 ug/ml PMID[14640527]
NPT574 Cell Line XF498 Homo sapiens ED50 = 38.07 ug/ml PMID[14640527]
NPT148 Cell Line HCT-15 Homo sapiens ED50 = 42.56 ug/ml PMID[14640527]

☑ 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 NPC477686 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
0.9762 High Similarity NPC191337
0.9024 High Similarity NPC111474
0.8913 High Similarity NPC118788
0.8913 High Similarity NPC15325
0.8864 High Similarity NPC166788
0.8537 High Similarity NPC180840
0.8293 Intermediate Similarity NPC185839
0.8261 Intermediate Similarity NPC8610
0.8261 Intermediate Similarity NPC262558
0.8222 Intermediate Similarity NPC25771
0.8125 Intermediate Similarity NPC228776
0.8049 Intermediate Similarity NPC38497
0.8 Intermediate Similarity NPC301972
0.8 Intermediate Similarity NPC216921
0.8 Intermediate Similarity NPC292463
0.7872 Intermediate Similarity NPC471752
0.7826 Intermediate Similarity NPC471753
0.7805 Intermediate Similarity NPC269641
0.7755 Intermediate Similarity NPC32351
0.7755 Intermediate Similarity NPC58970
0.7755 Intermediate Similarity NPC225974
0.7755 Intermediate Similarity NPC176819
0.7755 Intermediate Similarity NPC163984
0.7736 Intermediate Similarity NPC283502
0.7736 Intermediate Similarity NPC268185
0.7727 Intermediate Similarity NPC113082
0.7647 Intermediate Similarity NPC37644
0.7647 Intermediate Similarity NPC474805
0.7561 Intermediate Similarity NPC12889
0.7551 Intermediate Similarity NPC145311
0.75 Intermediate Similarity NPC217923
0.75 Intermediate Similarity NPC317796
0.75 Intermediate Similarity NPC100380
0.7451 Intermediate Similarity NPC137396
0.7407 Intermediate Similarity NPC299369
0.7407 Intermediate Similarity NPC224103
0.7407 Intermediate Similarity NPC200831
0.74 Intermediate Similarity NPC220191
0.7333 Intermediate Similarity NPC101147
0.7333 Intermediate Similarity NPC18205
0.7333 Intermediate Similarity NPC12319
0.7321 Intermediate Similarity NPC79756
0.7317 Intermediate Similarity NPC266979
0.7308 Intermediate Similarity NPC296311
0.7308 Intermediate Similarity NPC268564
0.7308 Intermediate Similarity NPC23117
0.7273 Intermediate Similarity NPC92863
0.7273 Intermediate Similarity NPC155880
0.7273 Intermediate Similarity NPC311852
0.7255 Intermediate Similarity NPC22329
0.7255 Intermediate Similarity NPC64866
0.7222 Intermediate Similarity NPC473733
0.72 Intermediate Similarity NPC267110
0.7115 Intermediate Similarity NPC471751
0.7083 Intermediate Similarity NPC267514
0.7083 Intermediate Similarity NPC145755
0.7069 Intermediate Similarity NPC477830
0.7059 Intermediate Similarity NPC474391
0.7059 Intermediate Similarity NPC288381
0.7059 Intermediate Similarity NPC20934
0.7045 Intermediate Similarity NPC24833
0.7 Intermediate Similarity NPC324812
0.7 Intermediate Similarity NPC91962
0.6981 Remote Similarity NPC14002
0.6981 Remote Similarity NPC45283
0.6949 Remote Similarity NPC34622
0.6949 Remote Similarity NPC474400
0.6923 Remote Similarity NPC477458
0.6923 Remote Similarity NPC234829
0.6905 Remote Similarity NPC304788
0.6889 Remote Similarity NPC130923
0.6852 Remote Similarity NPC189677
0.6852 Remote Similarity NPC300121
0.6852 Remote Similarity NPC322461
0.6852 Remote Similarity NPC5626
0.6842 Remote Similarity NPC203233
0.6842 Remote Similarity NPC473494
0.6833 Remote Similarity NPC251118
0.6833 Remote Similarity NPC98897
0.68 Remote Similarity NPC4079
0.68 Remote Similarity NPC236355
0.68 Remote Similarity NPC14917
0.68 Remote Similarity NPC308331
0.68 Remote Similarity NPC128280
0.6786 Remote Similarity NPC281230
0.6786 Remote Similarity NPC192843
0.678 Remote Similarity NPC288253
0.678 Remote Similarity NPC32285
0.678 Remote Similarity NPC477707
0.678 Remote Similarity NPC57463
0.678 Remote Similarity NPC151728
0.678 Remote Similarity NPC53109
0.678 Remote Similarity NPC143168
0.6735 Remote Similarity NPC6963
0.6735 Remote Similarity NPC304079
0.6731 Remote Similarity NPC236338
0.6727 Remote Similarity NPC275472
0.6721 Remote Similarity NPC16119
0.6721 Remote Similarity NPC137163
0.6667 Remote Similarity NPC295777
0.6667 Remote Similarity NPC69898
0.6667 Remote Similarity NPC254764
0.6667 Remote Similarity NPC7029
0.6667 Remote Similarity NPC150162
0.6667 Remote Similarity NPC4638
0.6667 Remote Similarity NPC474141
0.6667 Remote Similarity NPC139056
0.6667 Remote Similarity NPC471958
0.6667 Remote Similarity NPC217188
0.6667 Remote Similarity NPC320421
0.6667 Remote Similarity NPC212210
0.6613 Remote Similarity NPC474619
0.6613 Remote Similarity NPC106613
0.6613 Remote Similarity NPC203335
0.661 Remote Similarity NPC151648
0.661 Remote Similarity NPC97322
0.6607 Remote Similarity NPC325977
0.6604 Remote Similarity NPC30433
0.66 Remote Similarity NPC474202
0.66 Remote Similarity NPC474362
0.66 Remote Similarity NPC270706
0.6552 Remote Similarity NPC259261
0.6552 Remote Similarity NPC472304
0.6552 Remote Similarity NPC276764
0.6545 Remote Similarity NPC209431
0.6545 Remote Similarity NPC474127
0.6545 Remote Similarity NPC100809
0.6545 Remote Similarity NPC129710
0.6531 Remote Similarity NPC106819
0.6508 Remote Similarity NPC260474
0.6508 Remote Similarity NPC155198
0.6508 Remote Similarity NPC87141
0.6508 Remote Similarity NPC188292
0.65 Remote Similarity NPC322457
0.65 Remote Similarity NPC165695
0.6491 Remote Similarity NPC193695
0.6491 Remote Similarity NPC71755
0.6458 Remote Similarity NPC270170
0.6458 Remote Similarity NPC33489
0.6458 Remote Similarity NPC7754
0.6441 Remote Similarity NPC127582
0.6441 Remote Similarity NPC25853
0.6429 Remote Similarity NPC173157
0.6429 Remote Similarity NPC297280
0.6429 Remote Similarity NPC188789
0.6406 Remote Similarity NPC469914
0.6406 Remote Similarity NPC256846
0.6406 Remote Similarity NPC262673
0.64 Remote Similarity NPC106547
0.6383 Remote Similarity NPC33761
0.6379 Remote Similarity NPC170799
0.6379 Remote Similarity NPC281195
0.6379 Remote Similarity NPC94991
0.6379 Remote Similarity NPC266295
0.6379 Remote Similarity NPC308108
0.6379 Remote Similarity NPC60772
0.6379 Remote Similarity NPC56905
0.6379 Remote Similarity NPC27610
0.6379 Remote Similarity NPC30215
0.6364 Remote Similarity NPC168521
0.6349 Remote Similarity NPC243272
0.6349 Remote Similarity NPC475523
0.6333 Remote Similarity NPC475795
0.6333 Remote Similarity NPC260573
0.6333 Remote Similarity NPC64985
0.6333 Remote Similarity NPC213152
0.6327 Remote Similarity NPC298710
0.6327 Remote Similarity NPC208936
0.6327 Remote Similarity NPC67920
0.6327 Remote Similarity NPC287397
0.6308 Remote Similarity NPC94743
0.6308 Remote Similarity NPC291062
0.6308 Remote Similarity NPC2634
0.6308 Remote Similarity NPC251929
0.6308 Remote Similarity NPC265782
0.6304 Remote Similarity NPC279300
0.6304 Remote Similarity NPC220061
0.6296 Remote Similarity NPC27438
0.6296 Remote Similarity NPC43053
0.629 Remote Similarity NPC470688
0.629 Remote Similarity NPC470329
0.6279 Remote Similarity NPC3649
0.6275 Remote Similarity NPC110396
0.6275 Remote Similarity NPC117572
0.6271 Remote Similarity NPC106851
0.6271 Remote Similarity NPC96551
0.6271 Remote Similarity NPC329550
0.6271 Remote Similarity NPC285594
0.6271 Remote Similarity NPC274927
0.6271 Remote Similarity NPC38455
0.625 Remote Similarity NPC63396
0.625 Remote Similarity NPC323278
0.625 Remote Similarity NPC134385
0.625 Remote Similarity NPC202850
0.625 Remote Similarity NPC310992
0.625 Remote Similarity NPC146376
0.625 Remote Similarity NPC263382
0.625 Remote Similarity NPC125578
0.623 Remote Similarity NPC190049
0.623 Remote Similarity NPC474658

  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 NPC477686 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
0.8333 Intermediate Similarity NPD5783 Phase 3
0.7407 Intermediate Similarity NPD8779 Phase 3
0.678 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6727 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6721 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6538 Remote Similarity NPD4220 Pre-registration
0.6452 Remote Similarity NPD7331 Phase 2
0.6379 Remote Similarity NPD287 Approved
0.6349 Remote Similarity NPD3709 Clinical (unspecified phase)
0.6308 Remote Similarity NPD4691 Approved
0.6296 Remote Similarity NPD6927 Phase 3
0.6275 Remote Similarity NPD4222 Approved
0.6275 Remote Similarity NPD39 Approved
0.6275 Remote Similarity NPD3174 Discontinued
0.62 Remote Similarity NPD5326 Phase 3
0.6154 Remote Similarity NPD4137 Phase 3
0.6078 Remote Similarity NPD6097 Approved
0.6078 Remote Similarity NPD6096 Approved
0.6061 Remote Similarity NPD4747 Approved
0.6038 Remote Similarity NPD5343 Approved
0.6029 Remote Similarity NPD4058 Approved
0.597 Remote Similarity NPD5276 Approved
0.5965 Remote Similarity NPD539 Approved
0.5926 Remote Similarity NPD3173 Approved
0.5873 Remote Similarity NPD1984 Approved
0.5806 Remote Similarity NPD4191 Approved
0.5806 Remote Similarity NPD4192 Approved
0.5806 Remote Similarity NPD4194 Approved
0.5806 Remote Similarity NPD4193 Approved
0.5797 Remote Similarity NPD5733 Approved
0.5797 Remote Similarity NPD4687 Approved
0.5781 Remote Similarity NPD7341 Phase 2
0.5775 Remote Similarity NPD4756 Discovery
0.5714 Remote Similarity NPD29 Approved
0.5714 Remote Similarity NPD28 Approved
0.5692 Remote Similarity NPD3704 Approved
0.5686 Remote Similarity NPD9297 Discontinued
0.5686 Remote Similarity NPD9091 Suspended
0.566 Remote Similarity NPD4265 Approved
0.5625 Remote Similarity NPD319 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