Structure

Physi-Chem Properties

Molecular Weight:  292.24
Volume:  338.295
LogP:  5.749
LogD:  4.334
LogS:  -5.632
# Rotatable Bonds:  12
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.43
Synthetic Accessibility Score:  3.309
Fsp3:  0.737
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:  -4.715
MDCK Permeability:  1.947114651557058e-05
Pgp-inhibitor:  0.107
Pgp-substrate:  0.013
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.975
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.45
Plasma Protein Binding (PPB):  97.88831329345703%
Volume Distribution (VD):  1.095
Pgp-substrate:  1.463985800743103%

ADMET: Metabolism

CYP1A2-inhibitor:  0.304
CYP1A2-substrate:  0.713
CYP2C19-inhibitor:  0.67
CYP2C19-substrate:  0.89
CYP2C9-inhibitor:  0.315
CYP2C9-substrate:  0.946
CYP2D6-inhibitor:  0.207
CYP2D6-substrate:  0.55
CYP3A4-inhibitor:  0.66
CYP3A4-substrate:  0.42

ADMET: Excretion

Clearance (CL):  2.561
Half-life (T1/2):  0.188

ADMET: Toxicity

hERG Blockers:  0.05
Human Hepatotoxicity (H-HT):  0.389
Drug-inuced Liver Injury (DILI):  0.693
AMES Toxicity:  0.799
Rat Oral Acute Toxicity:  0.037
Maximum Recommended Daily Dose:  0.937
Skin Sensitization:  0.97
Carcinogencity:  0.569
Eye Corrosion:  0.622
Eye Irritation:  0.858
Respiratory Toxicity:  0.965

Download Data

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

  Natural Product: NPC477457

Natural Product ID:  NPC477457
Common Name*:   (1Z)-1-(2-undecyl-2,3-dihydropyran-6-ylidene)propan-2-one
IUPAC Name:   (1Z)-1-(2-undecyl-2,3-dihydropyran-6-ylidene)propan-2-one
Synonyms:  
Standard InCHIKey:  ZDOQVHVFJATDRW-MNDPQUGUSA-N
Standard InCHI:  InChI=1S/C19H32O2/c1-3-4-5-6-7-8-9-10-11-13-18-14-12-15-19(21-18)16-17(2)20/h12,15-16,18H,3-11,13-14H2,1-2H3/b19-16-
SMILES:  CCCCCCCCCCCC1CC=C/C(=C/C(=O)C)/O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   122181669
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans

*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
NPO11898 Lobophora variegata Species Dictyotaceae Eukaryota n.a. at depths of 630 m at El Mdano (Tenerife, Canary Islands) n.a. PMID[26126835]
NPO11898 Lobophora variegata Species Dictyotaceae 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
NPT1204 Organism Enterococcus faecalis ATCC 29212 Enterococcus faecalis ATCC 29212 Inhibition = 19 % PMID[26126835]
NPT19 Organism Escherichia coli Escherichia coli Inhibition = 25 % PMID[26126835]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus Inhibition = -57 % PMID[26126835]

☑ 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 NPC477457 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 NPC477456
0.8095 Intermediate Similarity NPC22897
0.8095 Intermediate Similarity NPC159650
0.7794 Intermediate Similarity NPC473752
0.7681 Intermediate Similarity NPC475760
0.7647 Intermediate Similarity NPC469446
0.7619 Intermediate Similarity NPC86948
0.75 Intermediate Similarity NPC185186
0.75 Intermediate Similarity NPC329890
0.75 Intermediate Similarity NPC329914
0.75 Intermediate Similarity NPC182794
0.75 Intermediate Similarity NPC327383
0.7424 Intermediate Similarity NPC299730
0.7424 Intermediate Similarity NPC26223
0.7361 Intermediate Similarity NPC475762
0.7324 Intermediate Similarity NPC475004
0.7313 Intermediate Similarity NPC68044
0.7297 Intermediate Similarity NPC285840
0.7297 Intermediate Similarity NPC327041
0.7297 Intermediate Similarity NPC260396
0.7273 Intermediate Similarity NPC474267
0.7246 Intermediate Similarity NPC471556
0.7222 Intermediate Similarity NPC64234
0.7222 Intermediate Similarity NPC476012
0.7222 Intermediate Similarity NPC476037
0.7222 Intermediate Similarity NPC37929
0.7206 Intermediate Similarity NPC210303
0.7206 Intermediate Similarity NPC179087
0.7206 Intermediate Similarity NPC44343
0.72 Intermediate Similarity NPC188860
0.7195 Intermediate Similarity NPC60765
0.7183 Intermediate Similarity NPC474823
0.7183 Intermediate Similarity NPC238223
0.7164 Intermediate Similarity NPC429928
0.7143 Intermediate Similarity NPC284447
0.7143 Intermediate Similarity NPC146811
0.7121 Intermediate Similarity NPC23418
0.7105 Intermediate Similarity NPC315394
0.7105 Intermediate Similarity NPC471225
0.7105 Intermediate Similarity NPC233071
0.7101 Intermediate Similarity NPC25747
0.7101 Intermediate Similarity NPC148233
0.7101 Intermediate Similarity NPC308457
0.7083 Intermediate Similarity NPC232812
0.7067 Intermediate Similarity NPC329826
0.7067 Intermediate Similarity NPC469414
0.7059 Intermediate Similarity NPC15193
0.7051 Intermediate Similarity NPC91332
0.7051 Intermediate Similarity NPC162741
0.7042 Intermediate Similarity NPC472266
0.7042 Intermediate Similarity NPC132286
0.7013 Intermediate Similarity NPC182292
0.7013 Intermediate Similarity NPC248775
0.7 Intermediate Similarity NPC471565
0.7 Intermediate Similarity NPC471566
0.7 Intermediate Similarity NPC288281
0.6986 Remote Similarity NPC477455
0.6986 Remote Similarity NPC316029
0.6986 Remote Similarity NPC315285
0.6986 Remote Similarity NPC469660
0.6944 Remote Similarity NPC218477
0.6944 Remote Similarity NPC313444
0.6923 Remote Similarity NPC25038
0.6923 Remote Similarity NPC470148
0.6923 Remote Similarity NPC1180
0.6923 Remote Similarity NPC139712
0.6923 Remote Similarity NPC180725
0.6923 Remote Similarity NPC470149
0.6912 Remote Similarity NPC154908
0.6912 Remote Similarity NPC127824
0.6912 Remote Similarity NPC252851
0.6912 Remote Similarity NPC143857
0.6912 Remote Similarity NPC226872
0.6912 Remote Similarity NPC158368
0.6912 Remote Similarity NPC229252
0.6901 Remote Similarity NPC124586
0.6901 Remote Similarity NPC191233
0.6901 Remote Similarity NPC16119
0.6892 Remote Similarity NPC133098
0.6883 Remote Similarity NPC474026
0.6875 Remote Similarity NPC10080
0.6875 Remote Similarity NPC123908
0.6849 Remote Similarity NPC470693
0.6849 Remote Similarity NPC151481
0.6842 Remote Similarity NPC315552
0.6835 Remote Similarity NPC470147
0.6835 Remote Similarity NPC133226
0.6818 Remote Similarity NPC221763
0.6806 Remote Similarity NPC474619
0.6806 Remote Similarity NPC203335
0.6806 Remote Similarity NPC225272
0.68 Remote Similarity NPC316851
0.68 Remote Similarity NPC474705
0.679 Remote Similarity NPC16488
0.6774 Remote Similarity NPC207815
0.6769 Remote Similarity NPC269615
0.6765 Remote Similarity NPC222852
0.6765 Remote Similarity NPC133600
0.6761 Remote Similarity NPC96414
0.6761 Remote Similarity NPC220766
0.6761 Remote Similarity NPC133904
0.6761 Remote Similarity NPC7940
0.6761 Remote Similarity NPC98897
0.6757 Remote Similarity NPC315597
0.6757 Remote Similarity NPC59558
0.675 Remote Similarity NPC184208
0.675 Remote Similarity NPC8538
0.675 Remote Similarity NPC315731
0.6719 Remote Similarity NPC106531
0.6716 Remote Similarity NPC471277
0.6716 Remote Similarity NPC471279
0.6714 Remote Similarity NPC217940
0.6712 Remote Similarity NPC477117
0.6711 Remote Similarity NPC470686
0.6709 Remote Similarity NPC271632
0.6709 Remote Similarity NPC473947
0.6667 Remote Similarity NPC315115
0.6667 Remote Similarity NPC474913
0.6667 Remote Similarity NPC201356
0.6667 Remote Similarity NPC113370
0.6667 Remote Similarity NPC316185
0.6667 Remote Similarity NPC293114
0.6667 Remote Similarity NPC275316
0.6667 Remote Similarity NPC475711
0.6667 Remote Similarity NPC316324
0.6667 Remote Similarity NPC248125
0.6667 Remote Similarity NPC84038
0.6667 Remote Similarity NPC79756
0.6667 Remote Similarity NPC476079
0.6667 Remote Similarity NPC103743
0.6627 Remote Similarity NPC307112
0.6622 Remote Similarity NPC143396
0.6622 Remote Similarity NPC101622
0.662 Remote Similarity NPC474400
0.662 Remote Similarity NPC34622
0.6618 Remote Similarity NPC469373
0.6585 Remote Similarity NPC475083
0.6582 Remote Similarity NPC326753
0.6579 Remote Similarity NPC222244
0.6579 Remote Similarity NPC16349
0.6579 Remote Similarity NPC284006
0.6571 Remote Similarity NPC26810
0.6571 Remote Similarity NPC325929
0.6571 Remote Similarity NPC151648
0.6571 Remote Similarity NPC320305
0.6571 Remote Similarity NPC328776
0.6571 Remote Similarity NPC271282
0.6571 Remote Similarity NPC66460
0.6567 Remote Similarity NPC150717
0.6552 Remote Similarity NPC32944
0.6552 Remote Similarity NPC193396
0.6548 Remote Similarity NPC47220
0.6548 Remote Similarity NPC316426
0.6548 Remote Similarity NPC315395
0.6548 Remote Similarity NPC186332
0.6548 Remote Similarity NPC208473
0.6543 Remote Similarity NPC112868
0.6538 Remote Similarity NPC301525
0.6538 Remote Similarity NPC261732
0.6533 Remote Similarity NPC94743
0.6533 Remote Similarity NPC291062
0.6533 Remote Similarity NPC4299
0.6528 Remote Similarity NPC245947
0.6528 Remote Similarity NPC326268
0.6528 Remote Similarity NPC136164
0.6528 Remote Similarity NPC318420
0.6528 Remote Similarity NPC255863
0.6522 Remote Similarity NPC286189
0.6522 Remote Similarity NPC478095
0.6515 Remote Similarity NPC478120
0.6512 Remote Similarity NPC210216
0.6512 Remote Similarity NPC95364
0.6512 Remote Similarity NPC142159
0.65 Remote Similarity NPC63649
0.65 Remote Similarity NPC472965
0.65 Remote Similarity NPC264227
0.65 Remote Similarity NPC471537
0.6494 Remote Similarity NPC227396
0.6494 Remote Similarity NPC477204
0.6494 Remote Similarity NPC107654
0.6494 Remote Similarity NPC92558
0.6494 Remote Similarity NPC315843
0.6494 Remote Similarity NPC474321
0.6486 Remote Similarity NPC276290
0.6486 Remote Similarity NPC272961
0.6486 Remote Similarity NPC470256
0.6479 Remote Similarity NPC57463
0.6479 Remote Similarity NPC29697
0.6479 Remote Similarity NPC2328
0.6479 Remote Similarity NPC151728
0.6479 Remote Similarity NPC474774
0.6477 Remote Similarity NPC189651
0.6477 Remote Similarity NPC475098
0.6477 Remote Similarity NPC248193
0.6471 Remote Similarity NPC199382
0.6471 Remote Similarity NPC313658
0.6471 Remote Similarity NPC316138
0.6471 Remote Similarity NPC474825
0.6471 Remote Similarity NPC44542
0.6471 Remote Similarity NPC125925

  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 NPC477457 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
0.6901 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6761 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6456 Remote Similarity NPD4756 Discovery
0.6429 Remote Similarity NPD4246 Clinical (unspecified phase)
0.641 Remote Similarity NPD8039 Approved
0.6389 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6265 Remote Similarity NPD5209 Approved
0.6232 Remote Similarity NPD8779 Phase 3
0.6067 Remote Similarity NPD7838 Discovery
0.6061 Remote Similarity NPD6927 Phase 3
0.6 Remote Similarity NPD3704 Approved
0.593 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5921 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5846 Remote Similarity NPD5343 Approved
0.5821 Remote Similarity NPD29 Approved
0.5821 Remote Similarity NPD28 Approved
0.5814 Remote Similarity NPD7154 Phase 3
0.5811 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5806 Remote Similarity NPD9297 Discontinued
0.5806 Remote Similarity NPD9091 Suspended
0.5789 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5733 Remote Similarity NPD3197 Phase 1
0.573 Remote Similarity NPD1282 Approved
0.5729 Remote Similarity NPD6648 Approved
0.5714 Remote Similarity NPD6698 Approved
0.5714 Remote Similarity NPD5785 Approved
0.5714 Remote Similarity NPD46 Approved
0.5682 Remote Similarity NPD1694 Approved
0.5647 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5647 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6096 Approved
0.5625 Remote Similarity NPD6097 Approved
0.561 Remote Similarity NPD8264 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