Structure

Physi-Chem Properties

Molecular Weight:  429.99
Volume:  322.242
LogP:  4.584
LogD:  3.977
LogS:  -4.585
# Rotatable Bonds:  1
TPSA:  29.46
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.612
Synthetic Accessibility Score:  5.027
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.534
MDCK Permeability:  1.7275422578677535e-05
Pgp-inhibitor:  0.987
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.03
20% Bioavailability (F20%):  0.017
30% Bioavailability (F30%):  0.424

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.748
Plasma Protein Binding (PPB):  94.014404296875%
Volume Distribution (VD):  1.582
Pgp-substrate:  10.913274765014648%

ADMET: Metabolism

CYP1A2-inhibitor:  0.308
CYP1A2-substrate:  0.725
CYP2C19-inhibitor:  0.327
CYP2C19-substrate:  0.886
CYP2C9-inhibitor:  0.899
CYP2C9-substrate:  0.121
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.381
CYP3A4-inhibitor:  0.464
CYP3A4-substrate:  0.825

ADMET: Excretion

Clearance (CL):  7.242
Half-life (T1/2):  0.231

ADMET: Toxicity

hERG Blockers:  0.047
Human Hepatotoxicity (H-HT):  0.921
Drug-inuced Liver Injury (DILI):  0.38
AMES Toxicity:  0.257
Rat Oral Acute Toxicity:  0.89
Maximum Recommended Daily Dose:  0.913
Skin Sensitization:  0.798
Carcinogencity:  0.661
Eye Corrosion:  0.932
Eye Irritation:  0.716
Respiratory Toxicity:  0.98

Download Data

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

  Natural Product: NPC83368

Natural Product ID:  NPC83368
Common Name*:   Caespitol
IUPAC Name:   (2R,3R,5R)-5-bromo-2-[(1S,3S,4S)-3-bromo-4-chloro-4-methylcyclohexyl]-2,6,6-trimethyloxan-3-ol
Synonyms:   Caespitol
Standard InCHIKey:  ZAULPZAMCNCFDT-SYPGZIFDSA-N
Standard InCHI:  InChI=1S/C15H25Br2ClO2/c1-13(2)10(16)8-12(19)15(4,20-13)9-5-6-14(3,18)11(17)7-9/h9-12,19H,5-8H2,1-4H3/t9-,10+,11-,12+,14-,15+/m0/s1
SMILES:  CC1(C)[C@@H](C[C@H]([C@@](C)([C@H]2CC[C@@](C)([C@H](C2)Br)Cl)O1)O)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL500561
PubChem CID:   14314413
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0002867] Alkyl halides
        • [CHEMONTID:0004485] Cyclohexyl halides

*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
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. tenerife n.a. PMID[10924166]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[16309323]
NPO29486 Laurencia catarinensis Species Rhodomelaceae Eukaryota n.a. Brazilian n.a. PMID[20039643]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[22220686]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[24279991]
NPO8821 Delphinium dictyocarpum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2491 Laurencia obtusa Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8821 Delphinium dictyocarpum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29486 Laurencia catarinensis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8821 Delphinium dictyocarpum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1054 Peucedanum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18938 Ladeania juncea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15600 Trifolium pannonicum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13493 Mauremys reevesii Species Geoemydidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2329 Scutellaria glabra Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1221 Juniperus serawschanica Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO666 Cymbidium aloifolium Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5527 Ligularia atroviolacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10341 Pseudogymnoascus pannorum Species Pseudeurotiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2491 Laurencia obtusa Species Rhodomelaceae 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
NPT1034 Cell Line Lu1 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[529551]
NPT91 Cell Line KB Homo sapiens IC50 > 25.0 ug.mL-1 PMID[529551]
NPT133 Cell Line ZR-75-1 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[529551]
NPT165 Cell Line HeLa Homo sapiens IC50 = 100.0 ug.mL-1 PMID[529551]
NPT165 Cell Line HeLa Homo sapiens IC50 = 26900.0 nM PMID[529552]
NPT165 Cell Line HeLa Homo sapiens IC50 = 30600.0 nM PMID[529552]
NPT1171 Cell Line HEp-2 Homo sapiens IC50 > 46000.0 nM PMID[529552]
NPT189 Cell Line Vero Chlorocebus aethiops IC50 = 25500.0 nM PMID[529552]
NPT189 Cell Line Vero Chlorocebus aethiops IC50 = 25800.0 nM PMID[529552]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 7600.0 nM PMID[529553]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 9700.0 nM PMID[529553]
NPT762 Cell Line A-431 Homo sapiens IC50 = 10200.0 nM PMID[529553]
NPT1234 Organism Chlorella fusca Chlorella fusca IZ = 3.0 mm PMID[529551]
NPT176 Organism Artemia salina Artemia salina Activity = 70.0 % PMID[529551]

☑ 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 NPC83368 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
0.8889 High Similarity NPC150938
0.8493 Intermediate Similarity NPC277993
0.8493 Intermediate Similarity NPC33876
0.8481 Intermediate Similarity NPC469555
0.8354 Intermediate Similarity NPC469556
0.8209 Intermediate Similarity NPC469582
0.8209 Intermediate Similarity NPC308569
0.8209 Intermediate Similarity NPC469572
0.7848 Intermediate Similarity NPC469580
0.7564 Intermediate Similarity NPC469581
0.7222 Intermediate Similarity NPC469573
0.7183 Intermediate Similarity NPC185116
0.7143 Intermediate Similarity NPC475934
0.6867 Remote Similarity NPC83436
0.6795 Remote Similarity NPC253123
0.6667 Remote Similarity NPC475786
0.6667 Remote Similarity NPC237510
0.6667 Remote Similarity NPC475793
0.6625 Remote Similarity NPC470173
0.6506 Remote Similarity NPC30575
0.6471 Remote Similarity NPC476603
0.64 Remote Similarity NPC475412
0.6364 Remote Similarity NPC273356
0.6364 Remote Similarity NPC97491
0.631 Remote Similarity NPC476606
0.631 Remote Similarity NPC470176
0.6279 Remote Similarity NPC31330
0.625 Remote Similarity NPC301725
0.6235 Remote Similarity NPC244002
0.619 Remote Similarity NPC476605
0.6133 Remote Similarity NPC47663
0.6118 Remote Similarity NPC470174
0.6092 Remote Similarity NPC329871
0.6071 Remote Similarity NPC166250
0.6044 Remote Similarity NPC313115
0.6024 Remote Similarity NPC157777
0.6024 Remote Similarity NPC131506
0.5955 Remote Similarity NPC5361
0.5952 Remote Similarity NPC476422
0.5952 Remote Similarity NPC476609
0.5949 Remote Similarity NPC94897
0.5942 Remote Similarity NPC223468
0.5942 Remote Similarity NPC287550
0.5942 Remote Similarity NPC176309
0.5942 Remote Similarity NPC147343
0.5942 Remote Similarity NPC84030
0.5942 Remote Similarity NPC198540
0.593 Remote Similarity NPC476607
0.5926 Remote Similarity NPC179823
0.5897 Remote Similarity NPC475807
0.5897 Remote Similarity NPC172622
0.5882 Remote Similarity NPC472944
0.5882 Remote Similarity NPC472945
0.5882 Remote Similarity NPC470151
0.5875 Remote Similarity NPC472946
0.5851 Remote Similarity NPC76909
0.5851 Remote Similarity NPC475817
0.5833 Remote Similarity NPC8004
0.5833 Remote Similarity NPC127283
0.5814 Remote Similarity NPC472952
0.5814 Remote Similarity NPC472950
0.5806 Remote Similarity NPC247826
0.5806 Remote Similarity NPC279260
0.5806 Remote Similarity NPC475276
0.5795 Remote Similarity NPC177343
0.5789 Remote Similarity NPC239453
0.5789 Remote Similarity NPC236588
0.5789 Remote Similarity NPC224552
0.5765 Remote Similarity NPC470660
0.5765 Remote Similarity NPC470659
0.5761 Remote Similarity NPC282598
0.5761 Remote Similarity NPC115995
0.575 Remote Similarity NPC476702
0.575 Remote Similarity NPC199937
0.5745 Remote Similarity NPC471377
0.5735 Remote Similarity NPC144891
0.5733 Remote Similarity NPC471269
0.5714 Remote Similarity NPC215175
0.5714 Remote Similarity NPC471879
0.5714 Remote Similarity NPC282454
0.5699 Remote Similarity NPC51267
0.5699 Remote Similarity NPC93616
0.5698 Remote Similarity NPC31046
0.5698 Remote Similarity NPC209666
0.5698 Remote Similarity NPC200167
0.5698 Remote Similarity NPC53868
0.5698 Remote Similarity NPC308489
0.5684 Remote Similarity NPC131453
0.5682 Remote Similarity NPC474574
0.5682 Remote Similarity NPC64081
0.5679 Remote Similarity NPC260116
0.5647 Remote Similarity NPC157422
0.5647 Remote Similarity NPC100586
0.5647 Remote Similarity NPC109457
0.5638 Remote Similarity NPC246347
0.5632 Remote Similarity NPC35397
0.5632 Remote Similarity NPC91387
0.5632 Remote Similarity NPC474946
0.5632 Remote Similarity NPC270306
0.5632 Remote Similarity NPC231680
0.5618 Remote Similarity NPC272841
0.5616 Remote Similarity NPC307022
0.5604 Remote Similarity NPC311891
0.56 Remote Similarity NPC156912

  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 NPC83368 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
0.68 Remote Similarity NPD371 Approved
0.5942 Remote Similarity NPD385 Approved
0.5942 Remote Similarity NPD384 Approved
0.5698 Remote Similarity NPD1810 Approved
0.5698 Remote Similarity NPD1811 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