Structure

Physi-Chem Properties

Molecular Weight:  214.06
Volume:  218.287
LogP:  3.057
LogD:  2.651
LogS:  -3.58
# Rotatable Bonds:  0
TPSA:  43.35
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.577
Synthetic Accessibility Score:  2.846
Fsp3:  0.154
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.763
MDCK Permeability:  1.650532976782415e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.995
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.766
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.023
Plasma Protein Binding (PPB):  78.77532196044922%
Volume Distribution (VD):  0.859
Pgp-substrate:  13.266083717346191%

ADMET: Metabolism

CYP1A2-inhibitor:  0.986
CYP1A2-substrate:  0.966
CYP2C19-inhibitor:  0.771
CYP2C19-substrate:  0.529
CYP2C9-inhibitor:  0.43
CYP2C9-substrate:  0.856
CYP2D6-inhibitor:  0.598
CYP2D6-substrate:  0.904
CYP3A4-inhibitor:  0.238
CYP3A4-substrate:  0.373

ADMET: Excretion

Clearance (CL):  7.252
Half-life (T1/2):  0.535

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.181
Drug-inuced Liver Injury (DILI):  0.752
AMES Toxicity:  0.476
Rat Oral Acute Toxicity:  0.093
Maximum Recommended Daily Dose:  0.917
Skin Sensitization:  0.575
Carcinogencity:  0.686
Eye Corrosion:  0.329
Eye Irritation:  0.978
Respiratory Toxicity:  0.265

Download Data

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

  Natural Product: NPC25038

Natural Product ID:  NPC25038
Common Name*:   Anhydrobarakol
IUPAC Name:   n.a.
Synonyms:   Anhydrobarakol
Standard InCHIKey:  XMBHPPIZLUISDL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H10O3/c1-7-3-9-5-10(14)6-12-13(9)11(15-7)4-8(2)16-12/h3-6H,1-2H3
SMILES:  Cc1oc2cc(C)oc3c2c(c1)cc(=O)c3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL457050
PubChem CID:   14429408
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003411] 2-benzopyrans

*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
NPO31100 Cassia siamea Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18524594]
NPO31100 Cassia siamea Species Fabaceae Eukaryota flowers n.a. n.a. PMID[19754128]
NPO31100 Cassia siamea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]

☑ 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
NPT165 Cell Line HeLa Homo sapiens IC50 > 100000.0 nM PMID[551957]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 7.8 ug.mL-1 PMID[551956]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 4700.0 nM PMID[551957]

☑ 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 NPC25038 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
0.8361 Intermediate Similarity NPC469446
0.7778 Intermediate Similarity NPC234084
0.7705 Intermediate Similarity NPC15193
0.7679 Intermediate Similarity NPC191643
0.7667 Intermediate Similarity NPC133600
0.7586 Intermediate Similarity NPC173157
0.7458 Intermediate Similarity NPC150717
0.7458 Intermediate Similarity NPC221763
0.7419 Intermediate Similarity NPC68044
0.7414 Intermediate Similarity NPC218486
0.7273 Intermediate Similarity NPC477117
0.7258 Intermediate Similarity NPC429928
0.7231 Intermediate Similarity NPC470033
0.7167 Intermediate Similarity NPC86948
0.7119 Intermediate Similarity NPC129710
0.7077 Intermediate Similarity NPC471566
0.7077 Intermediate Similarity NPC471556
0.7077 Intermediate Similarity NPC471565
0.7049 Intermediate Similarity NPC474825
0.7018 Intermediate Similarity NPC220191
0.7015 Intermediate Similarity NPC280374
0.6984 Remote Similarity NPC309408
0.6957 Remote Similarity NPC133098
0.6923 Remote Similarity NPC475618
0.6923 Remote Similarity NPC477456
0.6923 Remote Similarity NPC477457
0.6897 Remote Similarity NPC22329
0.6825 Remote Similarity NPC203233
0.6818 Remote Similarity NPC476589
0.6769 Remote Similarity NPC132243
0.6769 Remote Similarity NPC2328
0.6716 Remote Similarity NPC315115
0.6714 Remote Similarity NPC178575
0.6667 Remote Similarity NPC147621
0.6667 Remote Similarity NPC474805
0.6667 Remote Similarity NPC189700
0.6667 Remote Similarity NPC210258
0.6667 Remote Similarity NPC206507
0.6618 Remote Similarity NPC132286
0.6604 Remote Similarity NPC111474
0.6567 Remote Similarity NPC182794
0.6557 Remote Similarity NPC317796
0.6552 Remote Similarity NPC126184
0.6522 Remote Similarity NPC313444
0.6522 Remote Similarity NPC470032
0.6522 Remote Similarity NPC238223
0.6479 Remote Similarity NPC181587
0.6462 Remote Similarity NPC79756
0.6462 Remote Similarity NPC130953
0.6456 Remote Similarity NPC296589
0.6452 Remote Similarity NPC478117
0.6441 Remote Similarity NPC275316
0.641 Remote Similarity NPC288281
0.6379 Remote Similarity NPC128520
0.6377 Remote Similarity NPC470442
0.6338 Remote Similarity NPC315285
0.6338 Remote Similarity NPC316029
0.6338 Remote Similarity NPC315597
0.6338 Remote Similarity NPC59558
0.6324 Remote Similarity NPC220766
0.6324 Remote Similarity NPC7940
0.6324 Remote Similarity NPC131174
0.6316 Remote Similarity NPC270706
0.629 Remote Similarity NPC478120
0.6286 Remote Similarity NPC79220
0.6269 Remote Similarity NPC473737
0.6269 Remote Similarity NPC475073
0.625 Remote Similarity NPC299369
0.625 Remote Similarity NPC224103
0.625 Remote Similarity NPC200831
0.6232 Remote Similarity NPC191233
0.6232 Remote Similarity NPC37382
0.6212 Remote Similarity NPC98519
0.6212 Remote Similarity NPC476585
0.6207 Remote Similarity NPC128280
0.6203 Remote Similarity NPC475083
0.6197 Remote Similarity NPC470693
0.6167 Remote Similarity NPC15789
0.6167 Remote Similarity NPC236338
0.6164 Remote Similarity NPC316851
0.6143 Remote Similarity NPC203335
0.614 Remote Similarity NPC477686
0.614 Remote Similarity NPC106547
0.6129 Remote Similarity NPC168521
0.6119 Remote Similarity NPC151648
0.6094 Remote Similarity NPC51846
0.6087 Remote Similarity NPC133904
0.6078 Remote Similarity NPC12889
0.6061 Remote Similarity NPC22897
0.6061 Remote Similarity NPC286189
0.6061 Remote Similarity NPC473494
0.6061 Remote Similarity NPC159650
0.6056 Remote Similarity NPC287705
0.6053 Remote Similarity NPC54996
0.6053 Remote Similarity NPC316324
0.6053 Remote Similarity NPC473825
0.6049 Remote Similarity NPC281172
0.6049 Remote Similarity NPC307112
0.6034 Remote Similarity NPC191337
0.6034 Remote Similarity NPC110396
0.6034 Remote Similarity NPC166788
0.6034 Remote Similarity NPC47946
0.6034 Remote Similarity NPC26600
0.6029 Remote Similarity NPC179087
0.6029 Remote Similarity NPC44343
0.6029 Remote Similarity NPC210303
0.6 Remote Similarity NPC475555
0.6 Remote Similarity NPC15912
0.6 Remote Similarity NPC315552
0.6 Remote Similarity NPC135698
0.6 Remote Similarity NPC475675
0.5976 Remote Similarity NPC291712
0.5972 Remote Similarity NPC473277
0.5972 Remote Similarity NPC232812
0.597 Remote Similarity NPC26223
0.5968 Remote Similarity NPC46565
0.5968 Remote Similarity NPC229046
0.5968 Remote Similarity NPC137396
0.5949 Remote Similarity NPC312419
0.5942 Remote Similarity NPC471611
0.5932 Remote Similarity NPC197467
0.5921 Remote Similarity NPC470705
0.5921 Remote Similarity NPC263266
0.5909 Remote Similarity NPC139056
0.5904 Remote Similarity NPC103743
0.5904 Remote Similarity NPC476079
0.5904 Remote Similarity NPC113370
0.5902 Remote Similarity NPC27264
0.5897 Remote Similarity NPC271632
0.589 Remote Similarity NPC37929
0.589 Remote Similarity NPC64234
0.5882 Remote Similarity NPC266979
0.5882 Remote Similarity NPC212369
0.5875 Remote Similarity NPC10080
0.5875 Remote Similarity NPC123908
0.5862 Remote Similarity NPC25771
0.5857 Remote Similarity NPC476586
0.5857 Remote Similarity NPC273600
0.5844 Remote Similarity NPC471225
0.5844 Remote Similarity NPC315394
0.5833 Remote Similarity NPC474823
0.5833 Remote Similarity NPC90490
0.5821 Remote Similarity NPC302564
0.5811 Remote Similarity NPC5734
0.5806 Remote Similarity NPC148056
0.5797 Remote Similarity NPC57463
0.5797 Remote Similarity NPC474658
0.5797 Remote Similarity NPC151728
0.5797 Remote Similarity NPC476584
0.5789 Remote Similarity NPC478191
0.5789 Remote Similarity NPC478193
0.5789 Remote Similarity NPC57923
0.5789 Remote Similarity NPC478192
0.5789 Remote Similarity NPC478194
0.5789 Remote Similarity NPC478195
0.5789 Remote Similarity NPC478196
0.5781 Remote Similarity NPC151923
0.5781 Remote Similarity NPC9611
0.5781 Remote Similarity NPC151761
0.5781 Remote Similarity NPC159535
0.5769 Remote Similarity NPC99182
0.5765 Remote Similarity NPC95364
0.5765 Remote Similarity NPC142159
0.5765 Remote Similarity NPC210216
0.5758 Remote Similarity NPC268185
0.5753 Remote Similarity NPC151481
0.5753 Remote Similarity NPC475004
0.5738 Remote Similarity NPC82446
0.5735 Remote Similarity NPC19241
0.5733 Remote Similarity NPC287878
0.5714 Remote Similarity NPC151919
0.5714 Remote Similarity NPC125925
0.5714 Remote Similarity NPC308457
0.5714 Remote Similarity NPC25747
0.5714 Remote Similarity NPC53136
0.5714 Remote Similarity NPC148233
0.5714 Remote Similarity NPC34622
0.5714 Remote Similarity NPC474400
0.5714 Remote Similarity NPC173409
0.5714 Remote Similarity NPC150162
0.5698 Remote Similarity NPC280592
0.5698 Remote Similarity NPC224270
0.5698 Remote Similarity NPC274075
0.5698 Remote Similarity NPC213636
0.5698 Remote Similarity NPC253177
0.5694 Remote Similarity NPC21998
0.5694 Remote Similarity NPC225272
0.5692 Remote Similarity NPC297280
0.5692 Remote Similarity NPC474913
0.569 Remote Similarity NPC292463
0.5676 Remote Similarity NPC202011
0.5672 Remote Similarity NPC281195
0.5663 Remote Similarity NPC471060
0.566 Remote Similarity NPC269641
0.5658 Remote Similarity NPC470686
0.5652 Remote Similarity NPC217537
0.5647 Remote Similarity NPC478261
0.5647 Remote Similarity NPC478260
0.5647 Remote Similarity NPC478259
0.5645 Remote Similarity NPC118788

  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 NPC25038 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
0.625 Remote Similarity NPD8779 Phase 3
0.5806 Remote Similarity NPD6927 Phase 3
0.5789 Remote Similarity NPD9297 Discontinued
0.5789 Remote Similarity NPD9091 Suspended
0.5738 Remote Similarity NPD4220 Pre-registration
0.5641 Remote Similarity NPD4756 Discovery

  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