Structure

Physi-Chem Properties

Molecular Weight:  395.92
Volume:  273.604
LogP:  1.995
LogD:  2.287
LogS:  -3.651
# Rotatable Bonds:  2
TPSA:  57.9
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.718
Synthetic Accessibility Score:  4.359
Fsp3:  0.583
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.603
MDCK Permeability:  1.759614679031074e-05
Pgp-inhibitor:  0.988
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.174
20% Bioavailability (F20%):  0.056
30% Bioavailability (F30%):  0.372

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.714
Plasma Protein Binding (PPB):  95.5484619140625%
Volume Distribution (VD):  1.398
Pgp-substrate:  5.87558126449585%

ADMET: Metabolism

CYP1A2-inhibitor:  0.813
CYP1A2-substrate:  0.985
CYP2C19-inhibitor:  0.339
CYP2C19-substrate:  0.887
CYP2C9-inhibitor:  0.437
CYP2C9-substrate:  0.153
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.583
CYP3A4-inhibitor:  0.283
CYP3A4-substrate:  0.853

ADMET: Excretion

Clearance (CL):  3.418
Half-life (T1/2):  0.549

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.771
Drug-inuced Liver Injury (DILI):  0.955
AMES Toxicity:  0.658
Rat Oral Acute Toxicity:  0.938
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.486
Carcinogencity:  0.933
Eye Corrosion:  0.003
Eye Irritation:  0.026
Respiratory Toxicity:  0.826

Download Data

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

  Natural Product: NPC470032

Natural Product ID:  NPC470032
Common Name*:   Bromomethylchlamydosporol B
IUPAC Name:   (7R)-3,8-dibromo-4,7-dimethoxy-7,8-dimethyl-5H-pyrano[4,3-b]pyran-2-one
Synonyms:   Bromomethylchlamydosporol B
Standard InCHIKey:  LZWCFWLSHBIOLI-PIJUOVFKSA-N
Standard InCHI:  InChI=1S/C12H14Br2O5/c1-11(14)9-6(5-18-12(11,2)17-4)8(16-3)7(13)10(15)19-9/h5H2,1-4H3/t11?,12-/m1/s1
SMILES:  COc1c(Br)c(=O)oc2c1CO[C@@](C2(C)Br)(C)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1651323
PubChem CID:   53325562
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones and derivatives

*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
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[21090694]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[24175613]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25042 Fusarium tricinctum Species Nectriaceae 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 15.6 ug.mL-1 PMID[527220]

☑ 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 NPC470032 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
0.9385 High Similarity NPC280374
0.7971 Intermediate Similarity NPC470033
0.7647 Intermediate Similarity NPC15193
0.7432 Intermediate Similarity NPC178575
0.7368 Intermediate Similarity NPC206507
0.7368 Intermediate Similarity NPC210258
0.7368 Intermediate Similarity NPC147621
0.6849 Remote Similarity NPC476589
0.68 Remote Similarity NPC477117
0.6753 Remote Similarity NPC133098
0.6753 Remote Similarity NPC124072
0.6753 Remote Similarity NPC269103
0.6711 Remote Similarity NPC494
0.6667 Remote Similarity NPC132286
0.6623 Remote Similarity NPC299932
0.6623 Remote Similarity NPC475113
0.6622 Remote Similarity NPC475110
0.6579 Remote Similarity NPC238223
0.6538 Remote Similarity NPC162571
0.6538 Remote Similarity NPC112983
0.6528 Remote Similarity NPC309408
0.6522 Remote Similarity NPC25038
0.6438 Remote Similarity NPC217537
0.6429 Remote Similarity NPC221763
0.6429 Remote Similarity NPC150717
0.6375 Remote Similarity NPC188354
0.6364 Remote Similarity NPC234084
0.6324 Remote Similarity NPC191643
0.6301 Remote Similarity NPC476585
0.6286 Remote Similarity NPC173157
0.6267 Remote Similarity NPC53136
0.6267 Remote Similarity NPC173409
0.6267 Remote Similarity NPC471611
0.625 Remote Similarity NPC146583
0.6203 Remote Similarity NPC59558
0.6173 Remote Similarity NPC177030
0.6164 Remote Similarity NPC133600
0.6163 Remote Similarity NPC8161
0.6154 Remote Similarity NPC79220
0.6143 Remote Similarity NPC218486
0.6133 Remote Similarity NPC2328
0.6133 Remote Similarity NPC475073
0.6104 Remote Similarity NPC469446
0.6081 Remote Similarity NPC429928
0.6071 Remote Similarity NPC85743
0.6071 Remote Similarity NPC102065
0.6049 Remote Similarity NPC316851
0.6024 Remote Similarity NPC225022
0.6024 Remote Similarity NPC238554
0.6 Remote Similarity NPC315285
0.6 Remote Similarity NPC271632
0.5974 Remote Similarity NPC471566
0.5974 Remote Similarity NPC471565
0.5974 Remote Similarity NPC7940
0.5974 Remote Similarity NPC476586
0.5974 Remote Similarity NPC471556
0.5972 Remote Similarity NPC86948
0.5921 Remote Similarity NPC474729
0.5921 Remote Similarity NPC474723
0.5904 Remote Similarity NPC315552
0.5897 Remote Similarity NPC315115
0.5875 Remote Similarity NPC473277
0.5867 Remote Similarity NPC98519
0.5867 Remote Similarity NPC130953
0.5833 Remote Similarity NPC470705
0.5811 Remote Similarity NPC189700
0.5802 Remote Similarity NPC315597
0.5797 Remote Similarity NPC275316
0.5795 Remote Similarity NPC10080
0.5795 Remote Similarity NPC123908
0.5789 Remote Similarity NPC68044
0.5769 Remote Similarity NPC220766
0.5769 Remote Similarity NPC182794
0.5765 Remote Similarity NPC228902
0.5765 Remote Similarity NPC473825
0.5765 Remote Similarity NPC315394
0.5765 Remote Similarity NPC24827
0.5753 Remote Similarity NPC51846
0.575 Remote Similarity NPC313444
0.5732 Remote Similarity NPC181587
0.5732 Remote Similarity NPC316185
0.5714 Remote Similarity NPC473737
0.5714 Remote Similarity NPC476584
0.5696 Remote Similarity NPC37382
0.5696 Remote Similarity NPC191233
0.5694 Remote Similarity NPC151761
0.5694 Remote Similarity NPC159535
0.5694 Remote Similarity NPC478120
0.5679 Remote Similarity NPC470693
0.5679 Remote Similarity NPC151481
0.5658 Remote Similarity NPC79756
0.5658 Remote Similarity NPC26223
0.5647 Remote Similarity NPC271986
0.5641 Remote Similarity NPC471460
0.5641 Remote Similarity NPC308457
0.5641 Remote Similarity NPC475618
0.5641 Remote Similarity NPC25747
0.5641 Remote Similarity NPC148233
0.5638 Remote Similarity NPC327253
0.5632 Remote Similarity NPC199134
0.5632 Remote Similarity NPC286816
0.5618 Remote Similarity NPC474028
0.5618 Remote Similarity NPC474439
0.561 Remote Similarity NPC316029
0.5604 Remote Similarity NPC281172
0.5604 Remote Similarity NPC163606

  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 NPC470032 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
NPD

  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