Structure

Physi-Chem Properties

Molecular Weight:  540.1
Volume:  497.216
LogP:  5.208
LogD:  3.373
LogS:  -4.99
# Rotatable Bonds:  2
TPSA:  117.07
# H-Bond Aceptor:  7
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.136
Synthetic Accessibility Score:  5.687
Fsp3:  0.6
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  2

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.276
MDCK Permeability:  2.839356238837354e-05
Pgp-inhibitor:  0.034
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.026
20% Bioavailability (F20%):  0.062
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.021
Plasma Protein Binding (PPB):  95.3720932006836%
Volume Distribution (VD):  3.091
Pgp-substrate:  4.220851421356201%

ADMET: Metabolism

CYP1A2-inhibitor:  0.279
CYP1A2-substrate:  0.708
CYP2C19-inhibitor:  0.434
CYP2C19-substrate:  0.908
CYP2C9-inhibitor:  0.9
CYP2C9-substrate:  0.399
CYP2D6-inhibitor:  0.885
CYP2D6-substrate:  0.048
CYP3A4-inhibitor:  0.921
CYP3A4-substrate:  0.892

ADMET: Excretion

Clearance (CL):  1.133
Half-life (T1/2):  0.012

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.961
Drug-inuced Liver Injury (DILI):  0.973
AMES Toxicity:  0.964
Rat Oral Acute Toxicity:  0.74
Maximum Recommended Daily Dose:  0.953
Skin Sensitization:  0.292
Carcinogencity:  0.856
Eye Corrosion:  0.003
Eye Irritation:  0.027
Respiratory Toxicity:  0.994

Download Data

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

  Natural Product: NPC477995

Natural Product ID:  NPC477995
Common Name*:   7-Demethyl SF-245A-3
IUPAC Name:   (3R,4aR,10aS)-3,4a-dichloro-9-diazo-10a-[(2E)-3,7-dimethylocta-2,6-dienyl]-6-hydroxy-2,2-dimethyl-3,4-dihydrobenzo[g]chromene-5,8,10-trione
Synonyms:  
Standard InCHIKey:  JAQIWROMJCLPCP-DGGZCTJMSA-N
Standard InCHI:  InChI=1S/C25H28Cl2N2O5/c1-13(2)7-6-8-14(3)9-10-25-22(33)19-18(15(30)11-16(31)20(19)29-28)21(32)24(25,27)12-17(26)23(4,5)34-25/h7,9,11,17,30H,6,8,10,12H2,1-5H3/b14-9+/t17-,24+,25+/m1/s1
SMILES:  CC(=CCC/C(=C/C[C@]12C(=O)C3=C(C(=CC(=O)C3=[N+]=[N-])O)C(=O)[C@]1(C[C@H](C(O2)(C)C)Cl)Cl)/C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   135899067
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001640] Naphthopyrans
        • [CHEMONTID:0001641] Naphthopyranones

*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
NPO2873.1 Streptomyces antimycoticus nt17 Subspecies Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[18271555]

☑ 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 = 2000 nM PMID[18271555]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 1000 nM PMID[18271555]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 31600 nM PMID[18271555]
NPT1531 Organism Enterococcus faecium Enterococcus faecium MIC = 15800 nM PMID[18271555]
NPT1228 Organism Streptococcus pyogenes Streptococcus pyogenes MIC = 7800 nM PMID[18271555]

☑ 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 NPC477995 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
0.9417 High Similarity NPC477996
0.9333 High Similarity NPC471691
0.8943 High Similarity NPC471692
0.6642 Remote Similarity NPC473145
0.6567 Remote Similarity NPC245320
0.6519 Remote Similarity NPC476815
0.6519 Remote Similarity NPC31641
0.6508 Remote Similarity NPC473144
0.6508 Remote Similarity NPC297281
0.6385 Remote Similarity NPC20192
0.6378 Remote Similarity NPC131366
0.6377 Remote Similarity NPC16709
0.6357 Remote Similarity NPC232969
0.6357 Remote Similarity NPC199107
0.6319 Remote Similarity NPC78189
0.6296 Remote Similarity NPC243298
0.627 Remote Similarity NPC472972
0.625 Remote Similarity NPC230918
0.625 Remote Similarity NPC320294
0.625 Remote Similarity NPC269677
0.624 Remote Similarity NPC134083
0.622 Remote Similarity NPC470184
0.6198 Remote Similarity NPC474918
0.6194 Remote Similarity NPC321496
0.6194 Remote Similarity NPC472926
0.6183 Remote Similarity NPC168883
0.6174 Remote Similarity NPC473396
0.6154 Remote Similarity NPC85529
0.6154 Remote Similarity NPC32006
0.6148 Remote Similarity NPC261330
0.6142 Remote Similarity NPC185253
0.6142 Remote Similarity NPC215253
0.6136 Remote Similarity NPC300026
0.6111 Remote Similarity NPC471694
0.6111 Remote Similarity NPC471916
0.6094 Remote Similarity NPC224172
0.609 Remote Similarity NPC476290
0.6087 Remote Similarity NPC472933
0.6074 Remote Similarity NPC159333
0.6074 Remote Similarity NPC326264
0.6066 Remote Similarity NPC472688
0.6066 Remote Similarity NPC472676
0.6063 Remote Similarity NPC166770
0.6058 Remote Similarity NPC472927
0.6058 Remote Similarity NPC472934
0.6045 Remote Similarity NPC188738
0.6043 Remote Similarity NPC478051
0.604 Remote Similarity NPC473233
0.6032 Remote Similarity NPC272411
0.6015 Remote Similarity NPC470615
0.6015 Remote Similarity NPC87335
0.6015 Remote Similarity NPC250018
0.6014 Remote Similarity NPC251310
0.6014 Remote Similarity NPC478207
0.6014 Remote Similarity NPC21326
0.6014 Remote Similarity NPC287903
0.6 Remote Similarity NPC469515
0.6 Remote Similarity NPC476269
0.6 Remote Similarity NPC193948
0.5986 Remote Similarity NPC204639
0.5985 Remote Similarity NPC329869
0.5985 Remote Similarity NPC472925
0.5984 Remote Similarity NPC72397
0.5984 Remote Similarity NPC58271
0.5984 Remote Similarity NPC53454
0.5974 Remote Similarity NPC233770
0.5974 Remote Similarity NPC77481
0.5973 Remote Similarity NPC230889
0.597 Remote Similarity NPC210005
0.597 Remote Similarity NPC89408
0.5969 Remote Similarity NPC207885
0.5969 Remote Similarity NPC469851
0.5968 Remote Similarity NPC45579
0.5962 Remote Similarity NPC475837
0.5959 Remote Similarity NPC96425
0.5956 Remote Similarity NPC471204
0.5956 Remote Similarity NPC472929
0.595 Remote Similarity NPC203795
0.595 Remote Similarity NPC239685
0.5944 Remote Similarity NPC470973
0.5942 Remote Similarity NPC476190
0.594 Remote Similarity NPC322903
0.5935 Remote Similarity NPC36668
0.5935 Remote Similarity NPC118011
0.5935 Remote Similarity NPC68148
0.5935 Remote Similarity NPC65615
0.5932 Remote Similarity NPC474353
0.5932 Remote Similarity NPC275766
0.5926 Remote Similarity NPC171888
0.5926 Remote Similarity NPC34315
0.5926 Remote Similarity NPC207689
0.5926 Remote Similarity NPC476023
0.5926 Remote Similarity NPC146945
0.5923 Remote Similarity NPC39996
0.5923 Remote Similarity NPC469598
0.592 Remote Similarity NPC242637
0.5912 Remote Similarity NPC247069
0.5912 Remote Similarity NPC80650
0.5909 Remote Similarity NPC292588
0.5903 Remote Similarity NPC156797
0.5896 Remote Similarity NPC23497
0.5894 Remote Similarity NPC471672
0.5891 Remote Similarity NPC104861
0.5882 Remote Similarity NPC7797
0.5878 Remote Similarity NPC25666
0.5878 Remote Similarity NPC469980
0.5878 Remote Similarity NPC275583
0.5878 Remote Similarity NPC271059
0.5878 Remote Similarity NPC320154
0.5878 Remote Similarity NPC118902
0.5878 Remote Similarity NPC104161
0.5878 Remote Similarity NPC179208
0.5878 Remote Similarity NPC95899
0.5874 Remote Similarity NPC476729
0.5874 Remote Similarity NPC470922
0.5874 Remote Similarity NPC24651
0.5874 Remote Similarity NPC469494
0.5868 Remote Similarity NPC15807
0.5868 Remote Similarity NPC132228
0.5868 Remote Similarity NPC8518
0.5868 Remote Similarity NPC307112
0.5868 Remote Similarity NPC263997
0.5865 Remote Similarity NPC266514
0.5865 Remote Similarity NPC469853
0.5865 Remote Similarity NPC202524
0.5859 Remote Similarity NPC170131
0.5854 Remote Similarity NPC475001
0.5854 Remote Similarity NPC185059
0.5852 Remote Similarity NPC286880
0.585 Remote Similarity NPC476193
0.585 Remote Similarity NPC470185
0.5846 Remote Similarity NPC472637
0.5846 Remote Similarity NPC112613
0.5845 Remote Similarity NPC312833
0.584 Remote Similarity NPC73457
0.5839 Remote Similarity NPC474271
0.5839 Remote Similarity NPC7921
0.5839 Remote Similarity NPC208998
0.5833 Remote Similarity NPC213366
0.5833 Remote Similarity NPC40170
0.5827 Remote Similarity NPC31021
0.5827 Remote Similarity NPC216335
0.5827 Remote Similarity NPC27999
0.5827 Remote Similarity NPC227494
0.5827 Remote Similarity NPC91408
0.5827 Remote Similarity NPC477116
0.5824 Remote Similarity NPC131078
0.5824 Remote Similarity NPC311679
0.5822 Remote Similarity NPC110294
0.5821 Remote Similarity NPC476802
0.5821 Remote Similarity NPC89171
0.5816 Remote Similarity NPC476962
0.5816 Remote Similarity NPC112038
0.5812 Remote Similarity NPC248624
0.5809 Remote Similarity NPC38159
0.5809 Remote Similarity NPC317107
0.5809 Remote Similarity NPC115303
0.5809 Remote Similarity NPC472928
0.5809 Remote Similarity NPC324683
0.5804 Remote Similarity NPC67251
0.5804 Remote Similarity NPC18945
0.5804 Remote Similarity NPC120724
0.5804 Remote Similarity NPC105926
0.5804 Remote Similarity NPC265557
0.5804 Remote Similarity NPC91693
0.5802 Remote Similarity NPC80781
0.5802 Remote Similarity NPC235369
0.5798 Remote Similarity NPC225515
0.5798 Remote Similarity NPC55869
0.5793 Remote Similarity NPC476008
0.5789 Remote Similarity NPC478052
0.5789 Remote Similarity NPC469852
0.5789 Remote Similarity NPC469607
0.5789 Remote Similarity NPC1679
0.5786 Remote Similarity NPC297179
0.5786 Remote Similarity NPC17772
0.5786 Remote Similarity NPC470776
0.5781 Remote Similarity NPC93271
0.5781 Remote Similarity NPC135576
0.5781 Remote Similarity NPC94337
0.5778 Remote Similarity NPC77947
0.5778 Remote Similarity NPC286174
0.5778 Remote Similarity NPC471400
0.5778 Remote Similarity NPC141350
0.5778 Remote Similarity NPC220705
0.5776 Remote Similarity NPC472305
0.5775 Remote Similarity NPC315915
0.5772 Remote Similarity NPC476079
0.5772 Remote Similarity NPC220930
0.5772 Remote Similarity NPC272039
0.5772 Remote Similarity NPC103743
0.5772 Remote Similarity NPC113370
0.5769 Remote Similarity NPC269713
0.5769 Remote Similarity NPC46761
0.5766 Remote Similarity NPC317687
0.576 Remote Similarity NPC131864
0.576 Remote Similarity NPC475823
0.576 Remote Similarity NPC213636
0.576 Remote Similarity NPC280592
0.576 Remote Similarity NPC253177

  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 NPC477995 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
0.6148 Remote Similarity NPD5167 Approved
0.6115 Remote Similarity NPD5983 Phase 2
0.6084 Remote Similarity NPD6033 Approved
0.6014 Remote Similarity NPD8074 Phase 3
0.6 Remote Similarity NPD6914 Discontinued
0.5971 Remote Similarity NPD7100 Approved
0.5944 Remote Similarity NPD6336 Discontinued
0.5926 Remote Similarity NPD5215 Approved
0.592 Remote Similarity NPD5778 Approved
0.592 Remote Similarity NPD5779 Approved
0.5899 Remote Similarity NPD6314 Approved
0.5899 Remote Similarity NPD6313 Approved
0.5899 Remote Similarity NPD6335 Approved
0.587 Remote Similarity NPD6868 Approved
0.5857 Remote Similarity NPD7101 Approved
0.5852 Remote Similarity NPD5169 Approved
0.5827 Remote Similarity NPD5654 Approved
0.5821 Remote Similarity NPD5168 Approved
0.5809 Remote Similarity NPD5216 Approved
0.5809 Remote Similarity NPD5127 Approved
0.5809 Remote Similarity NPD5217 Approved
0.5794 Remote Similarity NPD5133 Approved
0.5782 Remote Similarity NPD5956 Approved
0.5745 Remote Similarity NPD4522 Approved
0.5736 Remote Similarity NPD5959 Approved
0.5682 Remote Similarity NPD5091 Approved
0.568 Remote Similarity NPD6101 Approved
0.568 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5649 Remote Similarity NPD6404 Discontinued
0.5638 Remote Similarity NPD7260 Phase 2
0.5625 Remote Similarity NPD5282 Discontinued
0.5612 Remote Similarity NPD4632 Approved
0.5603 Remote Similarity NPD7500 Approved
0.5603 Remote Similarity NPD6009 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