Structure

Physi-Chem Properties

Molecular Weight:  168.12
Volume:  191.187
LogP:  3.337
LogD:  2.147
LogS:  -2.777
# Rotatable Bonds:  4
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.655
Synthetic Accessibility Score:  2.931
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.791
MDCK Permeability:  3.170179479639046e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.873
30% Bioavailability (F30%):  0.886

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.184
Plasma Protein Binding (PPB):  82.9020004272461%
Volume Distribution (VD):  0.617
Pgp-substrate:  16.026355743408203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.042
CYP1A2-substrate:  0.089
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.278
CYP2C9-inhibitor:  0.016
CYP2C9-substrate:  0.955
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.147
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.088

ADMET: Excretion

Clearance (CL):  12.92
Half-life (T1/2):  0.889

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.919
Drug-inuced Liver Injury (DILI):  0.619
AMES Toxicity:  0.119
Rat Oral Acute Toxicity:  0.186
Maximum Recommended Daily Dose:  0.017
Skin Sensitization:  0.92
Carcinogencity:  0.734
Eye Corrosion:  0.992
Eye Irritation:  0.995
Respiratory Toxicity:  0.931

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  Natural Product: NPC304079

Natural Product ID:  NPC304079
Common Name*:   (2E)-3,7-Dimethylocta-2,6-Dienoic Acid
IUPAC Name:   (2E)-3,7-dimethylocta-2,6-dienoic acid
Synonyms:  
Standard InCHIKey:  ZHYZQXUYZJNEHD-VQHVLOKHSA-N
Standard InCHI:  InChI=1S/C10H16O2/c1-8(2)5-4-6-9(3)7-10(11)12/h5,7H,4,6H2,1-3H3,(H,11,12)/b9-7+
SMILES:  CC(=CCC/C(=C/C(=O)O)/C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL170190
PubChem CID:   5275520
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001127] Acyclic monoterpenoids

*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
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[15679319]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[17548953]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. aerial part n.a. PMID[18991207]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota Aerial parts n.a. n.a. PMID[20166702]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota essential oil Tibet n.a. PMID[20944522]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. exocarp n.a. PMID[21114277]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. aerial part n.a. PMID[21171571]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[24675423]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Bako, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Enemore, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Gedo, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Holleta, Ethiopia PMID[24926420]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota Twigs n.a. n.a. PMID[28541690]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. PMID[29094598]
NPO41973 A new engineered strain of Saccharomyces cerevisiae [10-gene cluster] Strain Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[29610307]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14470 Polypodium decumanum Species Polypodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13669 Hertia cheirifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14169 Acrocarpia paniculata Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13178 Ornithoglossum viride Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13876 Cedrela salvadorensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9569 Licaria chrysophylla Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5280 Rubia tetragona Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14369 Pocillopora eydouxi Species Pocilloporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4700 Pertusaria truncata Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12521 Sphaeranthus confertifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3013 Clathria basilana Species Microcionidae 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
NPT48 Individual Protein Lysine-specific demethylase 4D-like Homo sapiens Potency = 28183.8 nM PMID[479683]
NPT3 Individual Protein Thioredoxin glutathione reductase Schistosoma mansoni Potency = 56234.1 nM PMID[479683]
NPT524 Individual Protein Serine-protein kinase ATM Homo sapiens Potency = 39810.7 nM PMID[479683]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 100000.0 nM PMID[479683]
NPT11 Individual Protein Guanine nucleotide-binding protein G(s), subunit alpha Homo sapiens Potency n.a. 56234.1 nM PMID[479683]
NPT20 Organism Candida albicans Candida albicans Inhibition = 57.0 % PMID[479682]
NPT20 Organism Candida albicans Candida albicans IC50 > 100.0 ug.mL-1 PMID[479682]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 11689.1 nM PMID[479683]
NPT8 Individual Protein DNA polymerase iota Homo sapiens Potency n.a. 70794.6 nM PMID[479683]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 512.0 ug.mL-1 PMID[479684]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC = 512.0 ug.mL-1 PMID[479684]
NPT3721 Organism Enterococcus hirae Enterococcus hirae MIC = 512.0 ug.mL-1 PMID[479684]
NPT19 Organism Escherichia coli Escherichia coli MIC = 512.0 ug.mL-1 PMID[479684]
NPT19 Organism Escherichia coli Escherichia coli MIC > 512.0 ug.mL-1 PMID[479684]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 512.0 ug.mL-1 PMID[479684]

☑ 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 NPC304079 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
1.0 High Similarity NPC6963
0.9535 High Similarity NPC308331
0.8444 Intermediate Similarity NPC270706
0.8372 Intermediate Similarity NPC221250
0.8261 Intermediate Similarity NPC128280
0.82 Intermediate Similarity NPC474127
0.814 Intermediate Similarity NPC8270
0.8049 Intermediate Similarity NPC308418
0.7959 Intermediate Similarity NPC43053
0.7872 Intermediate Similarity NPC87137
0.7755 Intermediate Similarity NPC221467
0.7755 Intermediate Similarity NPC236338
0.7736 Intermediate Similarity NPC135863
0.7736 Intermediate Similarity NPC129150
0.7736 Intermediate Similarity NPC249850
0.7736 Intermediate Similarity NPC293437
0.7736 Intermediate Similarity NPC294938
0.7736 Intermediate Similarity NPC283502
0.766 Intermediate Similarity NPC26600
0.766 Intermediate Similarity NPC47946
0.7593 Intermediate Similarity NPC254095
0.7593 Intermediate Similarity NPC471619
0.7593 Intermediate Similarity NPC223679
0.7593 Intermediate Similarity NPC21946
0.75 Intermediate Similarity NPC255042
0.75 Intermediate Similarity NPC182840
0.75 Intermediate Similarity NPC197467
0.75 Intermediate Similarity NPC29091
0.75 Intermediate Similarity NPC103213
0.7455 Intermediate Similarity NPC82465
0.7255 Intermediate Similarity NPC15129
0.7234 Intermediate Similarity NPC116934
0.7222 Intermediate Similarity NPC472808
0.7222 Intermediate Similarity NPC324224
0.72 Intermediate Similarity NPC267110
0.72 Intermediate Similarity NPC135698
0.7193 Intermediate Similarity NPC317177
0.7193 Intermediate Similarity NPC329416
0.7193 Intermediate Similarity NPC326645
0.7193 Intermediate Similarity NPC317025
0.7174 Intermediate Similarity NPC269823
0.717 Intermediate Similarity NPC189677
0.717 Intermediate Similarity NPC478120
0.717 Intermediate Similarity NPC218486
0.7083 Intermediate Similarity NPC12907
0.7069 Intermediate Similarity NPC68110
0.7059 Intermediate Similarity NPC15789
0.7037 Intermediate Similarity NPC478117
0.7021 Intermediate Similarity NPC213538
0.7021 Intermediate Similarity NPC256766
0.6977 Remote Similarity NPC60675
0.6977 Remote Similarity NPC297363
0.6964 Remote Similarity NPC474084
0.6957 Remote Similarity NPC12319
0.6957 Remote Similarity NPC18205
0.6939 Remote Similarity NPC117572
0.6939 Remote Similarity NPC140501
0.6939 Remote Similarity NPC160628
0.6923 Remote Similarity NPC178586
0.6889 Remote Similarity NPC63598
0.6875 Remote Similarity NPC270796
0.6863 Remote Similarity NPC137419
0.6863 Remote Similarity NPC15912
0.6863 Remote Similarity NPC122212
0.6852 Remote Similarity NPC154626
0.6833 Remote Similarity NPC282760
0.6833 Remote Similarity NPC471565
0.6833 Remote Similarity NPC107258
0.6833 Remote Similarity NPC471556
0.6833 Remote Similarity NPC471566
0.6786 Remote Similarity NPC71755
0.6786 Remote Similarity NPC268185
0.678 Remote Similarity NPC473737
0.6744 Remote Similarity NPC12889
0.6739 Remote Similarity NPC15934
0.6735 Remote Similarity NPC477686
0.6735 Remote Similarity NPC138935
0.6731 Remote Similarity NPC288381
0.6731 Remote Similarity NPC20934
0.6731 Remote Similarity NPC27264
0.6731 Remote Similarity NPC225974
0.6721 Remote Similarity NPC242945
0.6721 Remote Similarity NPC308294
0.6721 Remote Similarity NPC259156
0.6721 Remote Similarity NPC81907
0.6721 Remote Similarity NPC142423
0.6721 Remote Similarity NPC315115
0.6667 Remote Similarity NPC185839
0.6667 Remote Similarity NPC209279
0.6667 Remote Similarity NPC67761
0.6667 Remote Similarity NPC180871
0.6667 Remote Similarity NPC68889
0.6667 Remote Similarity NPC57923
0.6667 Remote Similarity NPC51758
0.6667 Remote Similarity NPC194586
0.6667 Remote Similarity NPC34416
0.6667 Remote Similarity NPC189700
0.6667 Remote Similarity NPC91495
0.6667 Remote Similarity NPC102879
0.6667 Remote Similarity NPC88079
0.6667 Remote Similarity NPC108494
0.6613 Remote Similarity NPC254886
0.661 Remote Similarity NPC55376
0.661 Remote Similarity NPC26810
0.6604 Remote Similarity NPC48162
0.6604 Remote Similarity NPC148056
0.66 Remote Similarity NPC191337
0.66 Remote Similarity NPC474202
0.66 Remote Similarity NPC474362
0.6596 Remote Similarity NPC111474
0.6596 Remote Similarity NPC56917
0.6557 Remote Similarity NPC470123
0.6557 Remote Similarity NPC273600
0.6552 Remote Similarity NPC286189
0.6552 Remote Similarity NPC97570
0.6545 Remote Similarity NPC322461
0.6538 Remote Similarity NPC149821
0.6538 Remote Similarity NPC234084
0.6538 Remote Similarity NPC5413
0.6531 Remote Similarity NPC301972
0.6531 Remote Similarity NPC216921
0.6522 Remote Similarity NPC180840
0.6512 Remote Similarity NPC266979
0.6508 Remote Similarity NPC313444
0.65 Remote Similarity NPC475073
0.65 Remote Similarity NPC2328
0.65 Remote Similarity NPC77891
0.6491 Remote Similarity NPC44542
0.6491 Remote Similarity NPC472445
0.6491 Remote Similarity NPC265551
0.6491 Remote Similarity NPC212730
0.6481 Remote Similarity NPC151919
0.6481 Remote Similarity NPC191643
0.6471 Remote Similarity NPC8610
0.6471 Remote Similarity NPC262558
0.6471 Remote Similarity NPC42304
0.6452 Remote Similarity NPC255781
0.6452 Remote Similarity NPC322035
0.6452 Remote Similarity NPC166791
0.6452 Remote Similarity NPC100719
0.6444 Remote Similarity NPC38497
0.6441 Remote Similarity NPC79756
0.6441 Remote Similarity NPC130953
0.6429 Remote Similarity NPC49028
0.6429 Remote Similarity NPC173157
0.6429 Remote Similarity NPC474513
0.6429 Remote Similarity NPC317899
0.6429 Remote Similarity NPC146551
0.6429 Remote Similarity NPC470963
0.6429 Remote Similarity NPC152668
0.6429 Remote Similarity NPC67367
0.6415 Remote Similarity NPC289388
0.6415 Remote Similarity NPC474460
0.6415 Remote Similarity NPC59051
0.6406 Remote Similarity NPC151481
0.6406 Remote Similarity NPC236208
0.6383 Remote Similarity NPC217923
0.6364 Remote Similarity NPC477781
0.6364 Remote Similarity NPC217161
0.6364 Remote Similarity NPC98098
0.6364 Remote Similarity NPC217188
0.6364 Remote Similarity NPC477780
0.6364 Remote Similarity NPC224651
0.6349 Remote Similarity NPC132286
0.6346 Remote Similarity NPC207292
0.6333 Remote Similarity NPC151648
0.6333 Remote Similarity NPC64985
0.6327 Remote Similarity NPC206906
0.6327 Remote Similarity NPC304151
0.6327 Remote Similarity NPC187922
0.6316 Remote Similarity NPC325977
0.6316 Remote Similarity NPC96663
0.6316 Remote Similarity NPC245002
0.6316 Remote Similarity NPC311648
0.6316 Remote Similarity NPC470964
0.6316 Remote Similarity NPC221763
0.6308 Remote Similarity NPC315597
0.6308 Remote Similarity NPC59558
0.6308 Remote Similarity NPC316029
0.6304 Remote Similarity NPC107877
0.6296 Remote Similarity NPC28205
0.6296 Remote Similarity NPC244452
0.6296 Remote Similarity NPC474495
0.6296 Remote Similarity NPC473672
0.629 Remote Similarity NPC96414
0.629 Remote Similarity NPC7940
0.629 Remote Similarity NPC19769
0.6275 Remote Similarity NPC166788
0.6275 Remote Similarity NPC221379
0.6271 Remote Similarity NPC318306
0.6271 Remote Similarity NPC133600
0.6271 Remote Similarity NPC86789
0.6271 Remote Similarity NPC322186
0.6271 Remote Similarity NPC302564
0.6271 Remote Similarity NPC322002
0.625 Remote Similarity NPC151761
0.625 Remote Similarity NPC159535
0.625 Remote Similarity NPC123357
0.625 Remote Similarity NPC310210
0.625 Remote Similarity NPC238223

  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 NPC304079 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
0.9111 High Similarity NPD4220 Pre-registration
0.7609 Intermediate Similarity NPD9411 Phase 1
0.7193 Intermediate Similarity NPD4194 Approved
0.7193 Intermediate Similarity NPD4192 Approved
0.7193 Intermediate Similarity NPD4193 Approved
0.7193 Intermediate Similarity NPD4191 Approved
0.6939 Remote Similarity NPD4265 Approved
0.6939 Remote Similarity NPD39 Approved
0.6939 Remote Similarity NPD4222 Approved
0.6923 Remote Similarity NPD6927 Phase 3
0.6875 Remote Similarity NPD5326 Phase 3
0.6538 Remote Similarity NPD3173 Approved
0.6383 Remote Similarity NPD5783 Phase 3
0.6364 Remote Similarity NPD8573 Approved
0.6275 Remote Similarity NPD3174 Discontinued
0.6167 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6078 Remote Similarity NPD6097 Approved
0.6078 Remote Similarity NPD6096 Approved
0.6071 Remote Similarity NPD3172 Approved
0.6047 Remote Similarity NPD9114 Clinical (unspecified phase)
0.6038 Remote Similarity NPD5343 Approved
0.6032 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5965 Remote Similarity NPD3195 Phase 2
0.5965 Remote Similarity NPD3196 Approved
0.5965 Remote Similarity NPD3194 Approved
0.5965 Remote Similarity NPD4266 Approved
0.5818 Remote Similarity NPD2268 Discontinued
0.5775 Remote Similarity NPD4756 Discovery
0.5714 Remote Similarity NPD29 Approved
0.5714 Remote Similarity NPD28 Approved
0.569 Remote Similarity NPD539 Approved
0.5625 Remote Similarity NPD9115 Approved
0.5625 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5606 Remote Similarity NPD4247 Clinical (unspecified phase)
0.56 Remote Similarity NPD1153 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