Structure

Physi-Chem Properties

Molecular Weight:  258.16
Volume:  295.793
LogP:  5.283
LogD:  3.75
LogS:  -3.613
# Rotatable Bonds:  4
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.466
Synthetic Accessibility Score:  2.979
Fsp3:  0.294
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.878
MDCK Permeability:  2.62512439803686e-05
Pgp-inhibitor:  0.549
Pgp-substrate:  0.045
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.905
30% Bioavailability (F30%):  0.648

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.118
Plasma Protein Binding (PPB):  99.10818481445312%
Volume Distribution (VD):  5.568
Pgp-substrate:  1.896348237991333%

ADMET: Metabolism

CYP1A2-inhibitor:  0.948
CYP1A2-substrate:  0.891
CYP2C19-inhibitor:  0.708
CYP2C19-substrate:  0.529
CYP2C9-inhibitor:  0.406
CYP2C9-substrate:  0.951
CYP2D6-inhibitor:  0.87
CYP2D6-substrate:  0.922
CYP3A4-inhibitor:  0.359
CYP3A4-substrate:  0.235

ADMET: Excretion

Clearance (CL):  16.532
Half-life (T1/2):  0.876

ADMET: Toxicity

hERG Blockers:  0.061
Human Hepatotoxicity (H-HT):  0.954
Drug-inuced Liver Injury (DILI):  0.01
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.233
Maximum Recommended Daily Dose:  0.911
Skin Sensitization:  0.958
Carcinogencity:  0.28
Eye Corrosion:  0.018
Eye Irritation:  0.828
Respiratory Toxicity:  0.922

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

  Natural Product: NPC191337

Natural Product ID:  NPC191337
Common Name*:   2-[(2E)-3,7-Dimethyl-2,6-Octadienyl]-6-Methyl-2,5-Cyclohexadine-1,4-One
IUPAC Name:   2-[(2E)-3,7-dimethylocta-2,6-dienyl]-6-methylcyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  VDDALGSXMJYSIM-MDWZMJQESA-N
Standard InCHI:  InChI=1S/C17H22O2/c1-12(2)6-5-7-13(3)8-9-15-11-16(18)10-14(4)17(15)19/h6,8,10-11H,5,7,9H2,1-4H3/b13-8+
SMILES:  C/C(=CCC1=CC(=O)C=C(C1=O)C)/CCC=C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL470129
PubChem CID:   642530
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001534] Quinone and hydroquinone lipids
          • [CHEMONTID:0002802] Prenylquinones

*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
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. rhizome n.a. PMID[18787781]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[21302967]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27228227]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[9544564]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16087 Atractylodes lancea 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
NPT570 Individual Protein Arachidonate 5-lipoxygenase Homo sapiens IC50 = 200.0 nM PMID[452542]
NPT30 Individual Protein Cyclooxygenase-1 Homo sapiens IC50 = 64300.0 nM PMID[452542]

☑ 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 NPC191337 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 NPC477686
0.913 High Similarity NPC15325
0.881 High Similarity NPC111474
0.8723 High Similarity NPC118788
0.8667 High Similarity NPC166788
0.8478 Intermediate Similarity NPC262558
0.8478 Intermediate Similarity NPC8610
0.8444 Intermediate Similarity NPC25771
0.8333 Intermediate Similarity NPC228776
0.8333 Intermediate Similarity NPC180840
0.8222 Intermediate Similarity NPC301972
0.8222 Intermediate Similarity NPC292463
0.8095 Intermediate Similarity NPC185839
0.8085 Intermediate Similarity NPC471752
0.7959 Intermediate Similarity NPC58970
0.7959 Intermediate Similarity NPC176819
0.7959 Intermediate Similarity NPC32351
0.7959 Intermediate Similarity NPC163984
0.7955 Intermediate Similarity NPC113082
0.7925 Intermediate Similarity NPC283502
0.7857 Intermediate Similarity NPC38497
0.7843 Intermediate Similarity NPC37644
0.7826 Intermediate Similarity NPC216921
0.7755 Intermediate Similarity NPC145311
0.7727 Intermediate Similarity NPC217923
0.7708 Intermediate Similarity NPC100380
0.766 Intermediate Similarity NPC471753
0.7619 Intermediate Similarity NPC269641
0.76 Intermediate Similarity NPC225974
0.7593 Intermediate Similarity NPC268185
0.75 Intermediate Similarity NPC23117
0.75 Intermediate Similarity NPC92863
0.75 Intermediate Similarity NPC268564
0.75 Intermediate Similarity NPC474805
0.75 Intermediate Similarity NPC155880
0.75 Intermediate Similarity NPC296311
0.7455 Intermediate Similarity NPC311852
0.7451 Intermediate Similarity NPC64866
0.7407 Intermediate Similarity NPC473733
0.7381 Intermediate Similarity NPC12889
0.7358 Intermediate Similarity NPC317796
0.7308 Intermediate Similarity NPC137396
0.7308 Intermediate Similarity NPC471751
0.7292 Intermediate Similarity NPC267514
0.7292 Intermediate Similarity NPC145755
0.7273 Intermediate Similarity NPC200831
0.7273 Intermediate Similarity NPC299369
0.7273 Intermediate Similarity NPC224103
0.7255 Intermediate Similarity NPC20934
0.7255 Intermediate Similarity NPC474391
0.7255 Intermediate Similarity NPC288381
0.7255 Intermediate Similarity NPC220191
0.7241 Intermediate Similarity NPC477830
0.72 Intermediate Similarity NPC91962
0.72 Intermediate Similarity NPC324812
0.7193 Intermediate Similarity NPC79756
0.7174 Intermediate Similarity NPC18205
0.7174 Intermediate Similarity NPC12319
0.7174 Intermediate Similarity NPC101147
0.717 Intermediate Similarity NPC14002
0.717 Intermediate Similarity NPC45283
0.7143 Intermediate Similarity NPC266979
0.7119 Intermediate Similarity NPC474400
0.7119 Intermediate Similarity NPC34622
0.7115 Intermediate Similarity NPC22329
0.7115 Intermediate Similarity NPC234829
0.7115 Intermediate Similarity NPC477458
0.7059 Intermediate Similarity NPC267110
0.7037 Intermediate Similarity NPC189677
0.7037 Intermediate Similarity NPC5626
0.7037 Intermediate Similarity NPC322461
0.7018 Intermediate Similarity NPC473494
0.7 Intermediate Similarity NPC98897
0.7 Intermediate Similarity NPC14917
0.7 Intermediate Similarity NPC251118
0.7 Intermediate Similarity NPC4079
0.7 Intermediate Similarity NPC236355
0.6964 Remote Similarity NPC192843
0.6964 Remote Similarity NPC281230
0.6949 Remote Similarity NPC53109
0.6949 Remote Similarity NPC151728
0.6949 Remote Similarity NPC57463
0.6949 Remote Similarity NPC143168
0.6949 Remote Similarity NPC288253
0.6949 Remote Similarity NPC477707
0.6949 Remote Similarity NPC32285
0.6909 Remote Similarity NPC275472
0.6889 Remote Similarity NPC24833
0.6885 Remote Similarity NPC137163
0.6885 Remote Similarity NPC16119
0.6863 Remote Similarity NPC471958
0.6852 Remote Similarity NPC295777
0.6852 Remote Similarity NPC474141
0.6852 Remote Similarity NPC69898
0.6852 Remote Similarity NPC217188
0.6842 Remote Similarity NPC320421
0.6842 Remote Similarity NPC139056
0.6833 Remote Similarity NPC150162
0.6833 Remote Similarity NPC7029
0.6833 Remote Similarity NPC4638
0.6833 Remote Similarity NPC212210
0.68 Remote Similarity NPC474202
0.68 Remote Similarity NPC474362
0.6786 Remote Similarity NPC325977
0.678 Remote Similarity NPC97322
0.6774 Remote Similarity NPC203335
0.6774 Remote Similarity NPC474619
0.6774 Remote Similarity NPC106613
0.6744 Remote Similarity NPC304788
0.6739 Remote Similarity NPC130923
0.6727 Remote Similarity NPC209431
0.6727 Remote Similarity NPC300121
0.6727 Remote Similarity NPC100809
0.6724 Remote Similarity NPC203233
0.6724 Remote Similarity NPC472304
0.6724 Remote Similarity NPC259261
0.6724 Remote Similarity NPC276764
0.6667 Remote Similarity NPC7754
0.6667 Remote Similarity NPC155198
0.6667 Remote Similarity NPC270170
0.6667 Remote Similarity NPC188292
0.6667 Remote Similarity NPC128280
0.6667 Remote Similarity NPC260474
0.6667 Remote Similarity NPC322457
0.6667 Remote Similarity NPC165695
0.6667 Remote Similarity NPC87141
0.6667 Remote Similarity NPC193695
0.6667 Remote Similarity NPC33489
0.6667 Remote Similarity NPC308331
0.661 Remote Similarity NPC127582
0.661 Remote Similarity NPC25853
0.6607 Remote Similarity NPC297280
0.6607 Remote Similarity NPC188789
0.6604 Remote Similarity NPC236338
0.66 Remote Similarity NPC304079
0.66 Remote Similarity NPC6963
0.6596 Remote Similarity NPC33761
0.6562 Remote Similarity NPC262673
0.6562 Remote Similarity NPC469914
0.6562 Remote Similarity NPC256846
0.6552 Remote Similarity NPC60772
0.6552 Remote Similarity NPC56905
0.6552 Remote Similarity NPC30215
0.6552 Remote Similarity NPC308108
0.6552 Remote Similarity NPC170799
0.6552 Remote Similarity NPC27610
0.6552 Remote Similarity NPC94991
0.6552 Remote Similarity NPC266295
0.6531 Remote Similarity NPC67920
0.6531 Remote Similarity NPC298710
0.6531 Remote Similarity NPC287397
0.6531 Remote Similarity NPC208936
0.6522 Remote Similarity NPC220061
0.6522 Remote Similarity NPC254764
0.6512 Remote Similarity NPC3649
0.6508 Remote Similarity NPC475523
0.6508 Remote Similarity NPC243272
0.65 Remote Similarity NPC213152
0.65 Remote Similarity NPC475795
0.65 Remote Similarity NPC151648
0.65 Remote Similarity NPC64985
0.65 Remote Similarity NPC260573
0.6481 Remote Similarity NPC27438
0.6481 Remote Similarity NPC30433
0.6471 Remote Similarity NPC270706
0.6462 Remote Similarity NPC265782
0.6462 Remote Similarity NPC2634
0.6462 Remote Similarity NPC94743
0.6462 Remote Similarity NPC291062
0.6462 Remote Similarity NPC251929
0.6452 Remote Similarity NPC470329
0.6452 Remote Similarity NPC470688
0.6441 Remote Similarity NPC285594
0.6441 Remote Similarity NPC329550
0.6441 Remote Similarity NPC96551
0.6441 Remote Similarity NPC274927
0.6441 Remote Similarity NPC106851
0.6429 Remote Similarity NPC202850
0.6429 Remote Similarity NPC474127
0.6429 Remote Similarity NPC63396
0.6429 Remote Similarity NPC129710
0.6406 Remote Similarity NPC146376
0.6406 Remote Similarity NPC134385
0.6406 Remote Similarity NPC125578
0.6406 Remote Similarity NPC310992
0.6406 Remote Similarity NPC263382
0.64 Remote Similarity NPC106819
0.6393 Remote Similarity NPC190049
0.6393 Remote Similarity NPC167256
0.6379 Remote Similarity NPC71755
0.6379 Remote Similarity NPC321568
0.6379 Remote Similarity NPC208749
0.6379 Remote Similarity NPC115385
0.6379 Remote Similarity NPC281986
0.6379 Remote Similarity NPC22019
0.6364 Remote Similarity NPC474539
0.6364 Remote Similarity NPC54123
0.6346 Remote Similarity NPC195246
0.6346 Remote Similarity NPC276009
0.6346 Remote Similarity NPC22098

  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 NPC191337 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
0.814 Intermediate Similarity NPD5783 Phase 3
0.7273 Intermediate Similarity NPD8779 Phase 3
0.6949 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6909 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6885 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6613 Remote Similarity NPD7331 Phase 2
0.6552 Remote Similarity NPD287 Approved
0.6508 Remote Similarity NPD3709 Clinical (unspecified phase)
0.6471 Remote Similarity NPD3174 Discontinued
0.6471 Remote Similarity NPD39 Approved
0.6462 Remote Similarity NPD4691 Approved
0.6415 Remote Similarity NPD4220 Pre-registration
0.6308 Remote Similarity NPD4137 Phase 3
0.6212 Remote Similarity NPD4747 Approved
0.6182 Remote Similarity NPD6927 Phase 3
0.6176 Remote Similarity NPD4058 Approved
0.6154 Remote Similarity NPD4222 Approved
0.6119 Remote Similarity NPD5276 Approved
0.6111 Remote Similarity NPD3173 Approved
0.6078 Remote Similarity NPD5326 Phase 3
0.5968 Remote Similarity NPD4192 Approved
0.5968 Remote Similarity NPD4191 Approved
0.5968 Remote Similarity NPD4194 Approved
0.5968 Remote Similarity NPD4193 Approved
0.5962 Remote Similarity NPD6096 Approved
0.5962 Remote Similarity NPD6097 Approved
0.5942 Remote Similarity NPD5733 Approved
0.5942 Remote Similarity NPD4687 Approved
0.5938 Remote Similarity NPD7341 Phase 2
0.5926 Remote Similarity NPD5343 Approved
0.5915 Remote Similarity NPD4756 Discovery
0.5893 Remote Similarity NPD29 Approved
0.5893 Remote Similarity NPD28 Approved
0.5862 Remote Similarity NPD539 Approved
0.5846 Remote Similarity NPD3704 Approved
0.5833 Remote Similarity NPD319 Phase 1
0.5781 Remote Similarity NPD1984 Approved
0.569 Remote Similarity NPD3172 Approved
0.5676 Remote Similarity NPD4695 Discontinued
0.5672 Remote Similarity NPD3621 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