Structure

Physi-Chem Properties

Molecular Weight:  384.17
Volume:  368.954
LogP:  4.706
LogD:  4.006
LogS:  -4.377
# Rotatable Bonds:  7
TPSA:  32.76
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.362
Synthetic Accessibility Score:  4.948
Fsp3:  0.8
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:  -4.607
MDCK Permeability:  1.710977994662244e-05
Pgp-inhibitor:  0.953
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.407
30% Bioavailability (F30%):  0.016

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.478
Plasma Protein Binding (PPB):  88.20515441894531%
Volume Distribution (VD):  1.605
Pgp-substrate:  9.145230293273926%

ADMET: Metabolism

CYP1A2-inhibitor:  0.043
CYP1A2-substrate:  0.475
CYP2C19-inhibitor:  0.391
CYP2C19-substrate:  0.877
CYP2C9-inhibitor:  0.468
CYP2C9-substrate:  0.162
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.644
CYP3A4-inhibitor:  0.918
CYP3A4-substrate:  0.628

ADMET: Excretion

Clearance (CL):  4.892
Half-life (T1/2):  0.113

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.215
Drug-inuced Liver Injury (DILI):  0.292
AMES Toxicity:  0.033
Rat Oral Acute Toxicity:  0.294
Maximum Recommended Daily Dose:  0.202
Skin Sensitization:  0.17
Carcinogencity:  0.366
Eye Corrosion:  0.231
Eye Irritation:  0.163
Respiratory Toxicity:  0.917

Download Data

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

  Natural Product: NPC476607

Natural Product ID:  NPC476607
Common Name*:   2-Vinyl-4-[(1R)-2alpha-[2-(3,3-dimethyloxirane-2-yl)ethyl]-2-methyl-3beta-bromo-6-methylenecyclohexane-1beta-yl]-2-butanol
IUPAC Name:   5-[(1R,2S,3S)-3-bromo-2-[2-(3,3-dimethyloxiran-2-yl)ethyl]-2-methyl-6-methylidenecyclohexyl]-3-methylpent-1-en-3-ol
Synonyms:  
Standard InCHIKey:  YSEOBWHSSYMSKX-YREVAHRPSA-N
Standard InCHI:  InChI=1S/C20H33BrO2/c1-7-19(5,22)12-10-15-14(2)8-9-16(21)20(15,6)13-11-17-18(3,4)23-17/h7,15-17,22H,1-2,8-13H2,3-6H3/t15-,16+,17?,19?,20+/m1/s1
SMILES:  C[C@]1([C@H](CCC(=C)[C@H]1CCC(C)(C=C)O)Br)CCC2C(O2)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   122177951
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO18989 Aplysia depilans Species Aplysiidae Eukaryota n.a. Skyros Island (GPS coordinates 3887' N, 2457' E), in the North Sporades complex of the Aegean Sea, Greece 2011-AUG PMID[25814031]
NPO18989 Aplysia depilans Species Aplysiidae 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
NPT81 Cell Line A549 Homo sapiens IC50 > 100000 nM PMID[25814031]
NPT65 Cell Line HepG2 Homo sapiens IC50 = 53800 nM PMID[25814031]
NPT1718 Cell Line A431 Homo sapiens IC50 > 100000 nM PMID[25814031]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 71700 nM PMID[25814031]
NPT165 Cell Line HeLa Homo sapiens IC50 = 57900 nM PMID[25814031]

☑ 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 NPC476607 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
0.9296 High Similarity NPC476609
0.9178 High Similarity NPC476606
0.9041 High Similarity NPC476605
0.8873 High Similarity NPC476604
0.8571 High Similarity NPC476603
0.8378 Intermediate Similarity NPC475077
0.8077 Intermediate Similarity NPC476608
0.7875 Intermediate Similarity NPC476610
0.7778 Intermediate Similarity NPC113024
0.7703 Intermediate Similarity NPC476406
0.7683 Intermediate Similarity NPC311891
0.7632 Intermediate Similarity NPC9942
0.7471 Intermediate Similarity NPC131453
0.7471 Intermediate Similarity NPC188896
0.7397 Intermediate Similarity NPC41160
0.7356 Intermediate Similarity NPC174273
0.7342 Intermediate Similarity NPC329763
0.7179 Intermediate Similarity NPC74722
0.7179 Intermediate Similarity NPC304690
0.716 Intermediate Similarity NPC35397
0.716 Intermediate Similarity NPC474946
0.7126 Intermediate Similarity NPC313115
0.7108 Intermediate Similarity NPC215307
0.7108 Intermediate Similarity NPC476314
0.7108 Intermediate Similarity NPC274750
0.7089 Intermediate Similarity NPC34834
0.7073 Intermediate Similarity NPC265588
0.7037 Intermediate Similarity NPC71152
0.7024 Intermediate Similarity NPC476438
0.7024 Intermediate Similarity NPC129501
0.7024 Intermediate Similarity NPC233295
0.7024 Intermediate Similarity NPC192999
0.7013 Intermediate Similarity NPC279434
0.7011 Intermediate Similarity NPC474047
0.7 Intermediate Similarity NPC224552
0.7 Intermediate Similarity NPC239453
0.6977 Remote Similarity NPC123880
0.6977 Remote Similarity NPC471159
0.6974 Remote Similarity NPC225415
0.6962 Remote Similarity NPC329989
0.6962 Remote Similarity NPC239373
0.6944 Remote Similarity NPC39068
0.6941 Remote Similarity NPC474592
0.6941 Remote Similarity NPC15714
0.6923 Remote Similarity NPC69649
0.6923 Remote Similarity NPC68703
0.6923 Remote Similarity NPC259299
0.6915 Remote Similarity NPC156912
0.6897 Remote Similarity NPC475789
0.6897 Remote Similarity NPC477978
0.6883 Remote Similarity NPC258595
0.6867 Remote Similarity NPC268111
0.6842 Remote Similarity NPC283247
0.6835 Remote Similarity NPC471238
0.6835 Remote Similarity NPC245795
0.6835 Remote Similarity NPC305698
0.6835 Remote Similarity NPC276616
0.6829 Remote Similarity NPC201048
0.6829 Remote Similarity NPC476366
0.6829 Remote Similarity NPC306727
0.6824 Remote Similarity NPC72755
0.6824 Remote Similarity NPC476367
0.6818 Remote Similarity NPC306951
0.6809 Remote Similarity NPC257510
0.6809 Remote Similarity NPC299714
0.679 Remote Similarity NPC167706
0.679 Remote Similarity NPC471272
0.679 Remote Similarity NPC242001
0.6786 Remote Similarity NPC169994
0.6786 Remote Similarity NPC91594
0.6786 Remote Similarity NPC470711
0.6786 Remote Similarity NPC470758
0.6782 Remote Similarity NPC155521
0.6753 Remote Similarity NPC101128
0.6753 Remote Similarity NPC309300
0.6753 Remote Similarity NPC68656
0.6753 Remote Similarity NPC219940
0.6753 Remote Similarity NPC140233
0.6753 Remote Similarity NPC287744
0.675 Remote Similarity NPC210323
0.675 Remote Similarity NPC471560
0.6747 Remote Similarity NPC32832
0.6744 Remote Similarity NPC209944
0.6744 Remote Similarity NPC241290
0.6744 Remote Similarity NPC164840
0.6742 Remote Similarity NPC164424
0.6711 Remote Similarity NPC475251
0.6709 Remote Similarity NPC117607
0.6709 Remote Similarity NPC101307
0.6709 Remote Similarity NPC161612
0.6709 Remote Similarity NPC33583
0.6709 Remote Similarity NPC88454
0.6709 Remote Similarity NPC114651
0.6707 Remote Similarity NPC68443
0.6707 Remote Similarity NPC471799
0.6707 Remote Similarity NPC130665
0.6707 Remote Similarity NPC472506
0.6706 Remote Similarity NPC472342
0.6706 Remote Similarity NPC83351
0.6706 Remote Similarity NPC167891
0.6705 Remote Similarity NPC49208
0.6705 Remote Similarity NPC23748
0.6667 Remote Similarity NPC470766
0.6667 Remote Similarity NPC470749
0.6667 Remote Similarity NPC283316
0.6667 Remote Similarity NPC264245
0.6667 Remote Similarity NPC253190
0.6667 Remote Similarity NPC145498
0.6667 Remote Similarity NPC30575
0.6667 Remote Similarity NPC63958
0.6667 Remote Similarity NPC61080
0.6667 Remote Similarity NPC249423
0.6667 Remote Similarity NPC92231
0.6667 Remote Similarity NPC34732
0.6667 Remote Similarity NPC329626
0.6667 Remote Similarity NPC64123
0.6628 Remote Similarity NPC83436
0.6628 Remote Similarity NPC100906
0.6628 Remote Similarity NPC31330
0.6628 Remote Similarity NPC242767
0.6627 Remote Similarity NPC18819
0.6627 Remote Similarity NPC243342
0.6627 Remote Similarity NPC91858
0.6627 Remote Similarity NPC329090
0.6627 Remote Similarity NPC477138
0.6627 Remote Similarity NPC471797
0.6627 Remote Similarity NPC27395
0.6627 Remote Similarity NPC476736
0.6627 Remote Similarity NPC46610
0.6625 Remote Similarity NPC208999
0.6625 Remote Similarity NPC2648
0.6625 Remote Similarity NPC96484
0.6623 Remote Similarity NPC50435
0.6622 Remote Similarity NPC13789
0.6622 Remote Similarity NPC7491
0.6622 Remote Similarity NPC27853
0.6622 Remote Similarity NPC65786
0.6622 Remote Similarity NPC101285
0.6593 Remote Similarity NPC109900
0.6591 Remote Similarity NPC87489
0.6591 Remote Similarity NPC218616
0.6591 Remote Similarity NPC259858
0.6591 Remote Similarity NPC296701
0.6591 Remote Similarity NPC49964
0.6588 Remote Similarity NPC474826
0.6588 Remote Similarity NPC477426
0.6588 Remote Similarity NPC31037
0.6588 Remote Similarity NPC331618
0.6588 Remote Similarity NPC476703
0.6588 Remote Similarity NPC477425
0.6588 Remote Similarity NPC283619
0.6588 Remote Similarity NPC477427
0.6588 Remote Similarity NPC257191
0.6585 Remote Similarity NPC164045
0.6585 Remote Similarity NPC471271
0.6585 Remote Similarity NPC477792
0.6585 Remote Similarity NPC471662
0.6585 Remote Similarity NPC471268
0.6582 Remote Similarity NPC475897
0.6582 Remote Similarity NPC149680
0.6582 Remote Similarity NPC267027
0.6582 Remote Similarity NPC250977
0.6575 Remote Similarity NPC223604
0.6571 Remote Similarity NPC131623
0.6556 Remote Similarity NPC274448
0.6556 Remote Similarity NPC474189
0.6556 Remote Similarity NPC474349
0.6552 Remote Similarity NPC96362
0.6552 Remote Similarity NPC234193
0.6552 Remote Similarity NPC324772
0.6548 Remote Similarity NPC328104
0.6548 Remote Similarity NPC185536
0.6548 Remote Similarity NPC291503
0.6548 Remote Similarity NPC144075
0.6548 Remote Similarity NPC133580
0.6548 Remote Similarity NPC12696
0.6548 Remote Similarity NPC113639
0.6548 Remote Similarity NPC319090
0.6543 Remote Similarity NPC474248
0.6538 Remote Similarity NPC290367
0.6538 Remote Similarity NPC300593
0.6538 Remote Similarity NPC144650
0.6517 Remote Similarity NPC82623
0.6517 Remote Similarity NPC476927
0.6512 Remote Similarity NPC474216
0.6512 Remote Similarity NPC247783
0.6512 Remote Similarity NPC269543
0.6512 Remote Similarity NPC11908
0.6512 Remote Similarity NPC477089
0.6512 Remote Similarity NPC301707
0.6512 Remote Similarity NPC137587
0.6512 Remote Similarity NPC472501
0.6506 Remote Similarity NPC182717
0.6506 Remote Similarity NPC476709
0.6506 Remote Similarity NPC476422
0.6506 Remote Similarity NPC474140
0.65 Remote Similarity NPC308522
0.65 Remote Similarity NPC74885
0.65 Remote Similarity NPC253303
0.65 Remote Similarity NPC269077

  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 NPC476607 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
0.6705 Remote Similarity NPD6695 Phase 3
0.6629 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6627 Remote Similarity NPD6924 Approved
0.6627 Remote Similarity NPD6926 Approved
0.6552 Remote Similarity NPD6931 Approved
0.6552 Remote Similarity NPD6930 Phase 2
0.6512 Remote Similarity NPD7322 Clinical (unspecified phase)
0.6471 Remote Similarity NPD6933 Approved
0.6437 Remote Similarity NPD6929 Approved
0.6413 Remote Similarity NPD7750 Discontinued
0.6413 Remote Similarity NPD7524 Approved
0.6364 Remote Similarity NPD7514 Phase 3
0.6364 Remote Similarity NPD7332 Phase 2
0.6353 Remote Similarity NPD8264 Approved
0.6322 Remote Similarity NPD7145 Approved
0.6292 Remote Similarity NPD6902 Approved
0.6265 Remote Similarity NPD7144 Approved
0.6265 Remote Similarity NPD7143 Approved
0.625 Remote Similarity NPD7645 Phase 2
0.6207 Remote Similarity NPD5776 Phase 2
0.6207 Remote Similarity NPD6925 Approved
0.6207 Remote Similarity NPD6932 Approved
0.6196 Remote Similarity NPD6893 Approved
0.619 Remote Similarity NPD7150 Approved
0.619 Remote Similarity NPD7151 Approved
0.619 Remote Similarity NPD7152 Approved
0.618 Remote Similarity NPD7509 Discontinued
0.618 Remote Similarity NPD7525 Registered
0.6163 Remote Similarity NPD7339 Approved
0.6163 Remote Similarity NPD6942 Approved
0.6146 Remote Similarity NPD7087 Discontinued
0.6145 Remote Similarity NPD6923 Approved
0.6145 Remote Similarity NPD6922 Approved
0.6111 Remote Similarity NPD6898 Phase 1
0.6092 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6076 Remote Similarity NPD368 Approved
0.6047 Remote Similarity NPD4784 Approved
0.6047 Remote Similarity NPD4785 Approved
0.6 Remote Similarity NPD4243 Approved
0.5972 Remote Similarity NPD9410 Clinical (unspecified phase)
0.5895 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5889 Remote Similarity NPD6683 Phase 2
0.5825 Remote Similarity NPD5344 Discontinued
0.5816 Remote Similarity NPD7637 Suspended
0.5769 Remote Similarity NPD7632 Discontinued
0.575 Remote Similarity NPD1145 Discontinued
0.5747 Remote Similarity NPD4732 Discontinued
0.5745 Remote Similarity NPD4786 Approved
0.5728 Remote Similarity NPD6648 Approved
0.5714 Remote Similarity NPD4195 Approved
0.5714 Remote Similarity NPD342 Phase 1
0.5699 Remote Similarity NPD3667 Approved
0.5663 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5657 Remote Similarity NPD6411 Approved
0.5641 Remote Similarity NPD4219 Approved
0.5638 Remote Similarity NPD4788 Approved
0.5625 Remote Similarity NPD4623 Approved
0.5625 Remote Similarity NPD4519 Discontinued
0.5618 Remote Similarity NPD5275 Approved
0.5618 Remote Similarity NPD4190 Phase 3
0.5612 Remote Similarity NPD6051 Approved
0.5604 Remote Similarity NPD5784 Clinical (unspecified phase)
0.56 Remote Similarity NPD5778 Approved
0.56 Remote Similarity NPD5779 Approved
0.56 Remote Similarity NPD6399 Phase 3

  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