Structure

Physi-Chem Properties

Molecular Weight:  429.99
Volume:  322.242
LogP:  4.914
LogD:  4.072
LogS:  -4.068
# 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:  5.17
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:  -4.518
MDCK Permeability:  2.1719708456657827e-05
Pgp-inhibitor:  0.989
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.058
30% Bioavailability (F30%):  0.818

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.864
Plasma Protein Binding (PPB):  96.68630981445312%
Volume Distribution (VD):  1.753
Pgp-substrate:  7.114060401916504%

ADMET: Metabolism

CYP1A2-inhibitor:  0.132
CYP1A2-substrate:  0.541
CYP2C19-inhibitor:  0.167
CYP2C19-substrate:  0.904
CYP2C9-inhibitor:  0.657
CYP2C9-substrate:  0.095
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.508
CYP3A4-inhibitor:  0.306
CYP3A4-substrate:  0.574

ADMET: Excretion

Clearance (CL):  9.116
Half-life (T1/2):  0.282

ADMET: Toxicity

hERG Blockers:  0.059
Human Hepatotoxicity (H-HT):  0.746
Drug-inuced Liver Injury (DILI):  0.35
AMES Toxicity:  0.075
Rat Oral Acute Toxicity:  0.687
Maximum Recommended Daily Dose:  0.885
Skin Sensitization:  0.51
Carcinogencity:  0.75
Eye Corrosion:  0.956
Eye Irritation:  0.481
Respiratory Toxicity:  0.985

Download Data

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

  Natural Product: NPC150938

Natural Product ID:  NPC150938
Common Name*:   Isocaespitol
IUPAC Name:   (2S,3S,5S)-5-bromo-2-[(1R,3S,4S)-4-bromo-3-chloro-4-methylcyclohexyl]-2,6,6-trimethyloxan-3-ol
Synonyms:   Isocaespitol
Standard InCHIKey:  OVZBIWJSECOXAT-YLHZTVIJSA-N
Standard InCHI:  InChI=1S/C15H25Br2ClO2/c1-13(2)10(16)8-12(19)15(4,20-13)9-5-6-14(3,17)11(18)7-9/h9-12,19H,5-8H2,1-4H3/t9-,10+,11+,12+,14+,15+/m1/s1
SMILES:  O[C@H]1C[C@H](Br)C(O[C@@]1(C)[C@@H]1CC[C@]([C@H](C1)Cl)(C)Br)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1088006
PubChem CID:   46881070
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
NPO29486 Laurencia catarinensis Species Rhodomelaceae Eukaryota n.a. Brazilian n.a. PMID[20039643]
NPO29486 Laurencia catarinensis 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
NPT139 Cell Line HT-29 Homo sapiens IC50 > 100000.0 nM PMID[477631]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 100000.0 nM PMID[477631]
NPT762 Cell Line A-431 Homo sapiens IC50 > 100000.0 nM PMID[477631]

☑ 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 NPC150938 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 NPC83368
0.8261 Intermediate Similarity NPC469573
0.7619 Intermediate Similarity NPC469555
0.7564 Intermediate Similarity NPC33876
0.7564 Intermediate Similarity NPC277993
0.75 Intermediate Similarity NPC469556
0.7222 Intermediate Similarity NPC469582
0.7222 Intermediate Similarity NPC308569
0.7222 Intermediate Similarity NPC469572
0.7024 Intermediate Similarity NPC469580
0.6986 Remote Similarity NPC185116
0.6782 Remote Similarity NPC97491
0.6782 Remote Similarity NPC273356
0.6747 Remote Similarity NPC469581
0.6632 Remote Similarity NPC475934
0.6625 Remote Similarity NPC253123
0.6477 Remote Similarity NPC215175
0.6463 Remote Similarity NPC470173
0.631 Remote Similarity NPC237510
0.631 Remote Similarity NPC475793
0.6237 Remote Similarity NPC76909
0.6234 Remote Similarity NPC475412
0.6163 Remote Similarity NPC470176
0.6136 Remote Similarity NPC83436
0.6098 Remote Similarity NPC301725
0.6092 Remote Similarity NPC244002
0.6022 Remote Similarity NPC279260
0.5977 Remote Similarity NPC470174
0.5974 Remote Similarity NPC47663
0.5957 Remote Similarity NPC471377
0.5955 Remote Similarity NPC476603
0.593 Remote Similarity NPC166250
0.5914 Remote Similarity NPC93616
0.5904 Remote Similarity NPC475786
0.5882 Remote Similarity NPC131506
0.5882 Remote Similarity NPC157777
0.5851 Remote Similarity NPC246347
0.5824 Remote Similarity NPC5361
0.5802 Remote Similarity NPC94897
0.5795 Remote Similarity NPC476606
0.5795 Remote Similarity NPC30575
0.5783 Remote Similarity NPC179823
0.5778 Remote Similarity NPC329871
0.5778 Remote Similarity NPC31330
0.5775 Remote Similarity NPC147343
0.5775 Remote Similarity NPC176309
0.5775 Remote Similarity NPC223468
0.5775 Remote Similarity NPC198540
0.5775 Remote Similarity NPC84030
0.5775 Remote Similarity NPC287550
0.575 Remote Similarity NPC475807
0.575 Remote Similarity NPC172622
0.5747 Remote Similarity NPC472945
0.5747 Remote Similarity NPC472944
0.5747 Remote Similarity NPC470151
0.5745 Remote Similarity NPC313115
0.5732 Remote Similarity NPC472946
0.5698 Remote Similarity NPC127283
0.5698 Remote Similarity NPC8004
0.5684 Remote Similarity NPC247826
0.5682 Remote Similarity NPC476605
0.5682 Remote Similarity NPC472952
0.5682 Remote Similarity NPC472950
0.5667 Remote Similarity NPC177343
0.5641 Remote Similarity NPC236588
0.5638 Remote Similarity NPC115995
0.5632 Remote Similarity NPC470659
0.5632 Remote Similarity NPC470660
0.5632 Remote Similarity NPC476422
0.561 Remote Similarity NPC199937
0.561 Remote Similarity NPC476702

  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 NPC150938 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
0.6623 Remote Similarity NPD371 Approved
0.5775 Remote Similarity NPD385 Approved
0.5775 Remote Similarity NPD384 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