Structure

Physi-Chem Properties

Molecular Weight:  457.18
Volume:  452.649
LogP:  3.972
LogD:  3.19
LogS:  -3.745
# Rotatable Bonds:  10
TPSA:  86.63
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.273
Synthetic Accessibility Score:  5.513
Fsp3:  0.652
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.749
MDCK Permeability:  2.5892424673656933e-05
Pgp-inhibitor:  0.943
Pgp-substrate:  0.155
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.966
Plasma Protein Binding (PPB):  96.6750259399414%
Volume Distribution (VD):  1.339
Pgp-substrate:  3.323172092437744%

ADMET: Metabolism

CYP1A2-inhibitor:  0.049
CYP1A2-substrate:  0.709
CYP2C19-inhibitor:  0.669
CYP2C19-substrate:  0.765
CYP2C9-inhibitor:  0.638
CYP2C9-substrate:  0.605
CYP2D6-inhibitor:  0.104
CYP2D6-substrate:  0.188
CYP3A4-inhibitor:  0.938
CYP3A4-substrate:  0.328

ADMET: Excretion

Clearance (CL):  2.573
Half-life (T1/2):  0.845

ADMET: Toxicity

hERG Blockers:  0.045
Human Hepatotoxicity (H-HT):  0.49
Drug-inuced Liver Injury (DILI):  0.04
AMES Toxicity:  0.094
Rat Oral Acute Toxicity:  0.475
Maximum Recommended Daily Dose:  0.944
Skin Sensitization:  0.948
Carcinogencity:  0.724
Eye Corrosion:  0.004
Eye Irritation:  0.047
Respiratory Toxicity:  0.891

Download Data

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

  Natural Product: NPC96425

Natural Product ID:  NPC96425
Common Name*:   Gymnastatin R
IUPAC Name:   (2E,4E,6R)-N-[(1R,5R,6S,7S)-3,5-dichloro-1,6-dihydroxy-4-oxo-7-bicyclo[3.3.1]non-2-enyl]-4,6-dimethyldodeca-2,4-dienamide
Synonyms:   Gymnastatin R
Standard InCHIKey:  WDCSNVYLZCMUNB-WFXSWVRYSA-N
Standard InCHI:  InChI=1S/C23H33Cl2NO4/c1-4-5-6-7-8-15(2)11-16(3)9-10-19(27)26-18-13-22(30)12-17(24)20(28)23(25,14-22)21(18)29/h9-12,15,18,21,29-30H,4-8,13-14H2,1-3H3,(H,26,27)/b10-9+,16-11+/t15-,18+,21+,22-,23+/m1/s1
SMILES:  CCCCCC[C@@H](C)/C=C(C)/C=C/C(=N[C@H]1C[C@@]2(C=C(C(=O)[C@@](C2)([C@H]1O)Cl)Cl)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL255896
PubChem CID:   24854449
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones
              • [CHEMONTID:0004325] Cyclohexenones

*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
NPO33119 gymnascella dankaliensis Species Gymnoascaceae Eukaryota n.a. n.a. n.a. PMID[17067147]
NPO33119 gymnascella dankaliensis Species Gymnoascaceae Eukaryota n.a. n.a. n.a. PMID[17988094]
NPO33119 gymnascella dankaliensis Species Gymnoascaceae Eukaryota n.a. n.a. n.a. PMID[18284207]
NPO33119 gymnascella dankaliensis Species Gymnoascaceae Eukaryota n.a. n.a. n.a. PMID[25600409]

☑ 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
NPT168 Cell Line P388 Mus musculus ED50 = 2.8 ug ml-1 PMID[488393]

☑ 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 NPC96425 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
0.9023 High Similarity NPC77481
0.9023 High Similarity NPC233770
0.8028 Intermediate Similarity NPC475837
0.7786 Intermediate Similarity NPC16709
0.7286 Intermediate Similarity NPC78189
0.7133 Intermediate Similarity NPC230889
0.7122 Intermediate Similarity NPC121601
0.7122 Intermediate Similarity NPC471471
0.7122 Intermediate Similarity NPC164476
0.6596 Remote Similarity NPC204639
0.6565 Remote Similarity NPC472615
0.6538 Remote Similarity NPC474563
0.6519 Remote Similarity NPC7797
0.6493 Remote Similarity NPC476290
0.6486 Remote Similarity NPC472430
0.6466 Remote Similarity NPC307903
0.6466 Remote Similarity NPC140251
0.6449 Remote Similarity NPC216335
0.6439 Remote Similarity NPC472433
0.6418 Remote Similarity NPC133729
0.6397 Remote Similarity NPC476269
0.6364 Remote Similarity NPC472616
0.6358 Remote Similarity NPC208725
0.6357 Remote Similarity NPC323532
0.635 Remote Similarity NPC122404
0.6309 Remote Similarity NPC472428
0.622 Remote Similarity NPC472613
0.6214 Remote Similarity NPC476190
0.6165 Remote Similarity NPC297281
0.6165 Remote Similarity NPC473144
0.6164 Remote Similarity NPC204556
0.6131 Remote Similarity NPC92829
0.6131 Remote Similarity NPC328052
0.6131 Remote Similarity NPC46764
0.6122 Remote Similarity NPC471586
0.6103 Remote Similarity NPC168733
0.6099 Remote Similarity NPC147707
0.609 Remote Similarity NPC469598
0.609 Remote Similarity NPC128501
0.6071 Remote Similarity NPC24462
0.6056 Remote Similarity NPC9714
0.6054 Remote Similarity NPC287903
0.6049 Remote Similarity NPC100612
0.6049 Remote Similarity NPC187497
0.6049 Remote Similarity NPC113620
0.6049 Remote Similarity NPC475599
0.6049 Remote Similarity NPC174336
0.6047 Remote Similarity NPC299100
0.6043 Remote Similarity NPC469865
0.6015 Remote Similarity NPC115862
0.6015 Remote Similarity NPC282524
0.6 Remote Similarity NPC259476
0.6 Remote Similarity NPC116057
0.6 Remote Similarity NPC180950
0.5988 Remote Similarity NPC265699
0.5988 Remote Similarity NPC475527
0.5984 Remote Similarity NPC472983
0.5959 Remote Similarity NPC280498
0.5959 Remote Similarity NPC477995
0.5957 Remote Similarity NPC476814
0.5957 Remote Similarity NPC476813
0.5949 Remote Similarity NPC214821
0.5949 Remote Similarity NPC298067
0.5946 Remote Similarity NPC156797
0.5944 Remote Similarity NPC471673
0.594 Remote Similarity NPC215253
0.594 Remote Similarity NPC185253
0.5938 Remote Similarity NPC134321
0.5923 Remote Similarity NPC116930
0.5923 Remote Similarity NPC78159
0.5912 Remote Similarity NPC475800
0.5912 Remote Similarity NPC169375
0.5912 Remote Similarity NPC251330
0.5906 Remote Similarity NPC471791
0.5906 Remote Similarity NPC316186
0.5906 Remote Similarity NPC471793
0.5901 Remote Similarity NPC36463
0.5901 Remote Similarity NPC298005
0.5894 Remote Similarity NPC477996
0.5891 Remote Similarity NPC472978
0.5891 Remote Similarity NPC142838
0.5891 Remote Similarity NPC314500
0.5886 Remote Similarity NPC193753
0.5886 Remote Similarity NPC160222
0.5882 Remote Similarity NPC118911
0.5875 Remote Similarity NPC61717
0.5875 Remote Similarity NPC244380
0.5874 Remote Similarity NPC316325
0.5871 Remote Similarity NPC113325
0.5871 Remote Similarity NPC279045
0.587 Remote Similarity NPC102843
0.5865 Remote Similarity NPC103051
0.5865 Remote Similarity NPC166770
0.5862 Remote Similarity NPC477140
0.5862 Remote Similarity NPC477143
0.5859 Remote Similarity NPC472973
0.5845 Remote Similarity NPC471645
0.5844 Remote Similarity NPC145899
0.5839 Remote Similarity NPC32006
0.5839 Remote Similarity NPC271269
0.5839 Remote Similarity NPC85529
0.5839 Remote Similarity NPC128828
0.5833 Remote Similarity NPC301534
0.5833 Remote Similarity NPC250757
0.5828 Remote Similarity NPC471691
0.5827 Remote Similarity NPC474725
0.5827 Remote Similarity NPC473578
0.5827 Remote Similarity NPC472614
0.5817 Remote Similarity NPC76999
0.5814 Remote Similarity NPC128672
0.5809 Remote Similarity NPC72151
0.5809 Remote Similarity NPC475050
0.5806 Remote Similarity NPC228511
0.5802 Remote Similarity NPC472976
0.5802 Remote Similarity NPC474690
0.5802 Remote Similarity NPC472977
0.58 Remote Similarity NPC329919
0.58 Remote Similarity NPC477352
0.58 Remote Similarity NPC477793
0.5789 Remote Similarity NPC471692
0.5789 Remote Similarity NPC474938
0.5789 Remote Similarity NPC134083
0.5789 Remote Similarity NPC125771
0.5789 Remote Similarity NPC218902
0.5789 Remote Similarity NPC474785
0.5786 Remote Similarity NPC122926
0.5786 Remote Similarity NPC193579
0.5786 Remote Similarity NPC113012
0.5786 Remote Similarity NPC298469
0.5779 Remote Similarity NPC75318
0.5778 Remote Similarity NPC470184
0.5769 Remote Similarity NPC200788
0.5769 Remote Similarity NPC73457
0.5769 Remote Similarity NPC243680
0.5758 Remote Similarity NPC476245
0.5755 Remote Similarity NPC475150
0.5748 Remote Similarity NPC472974
0.5748 Remote Similarity NPC194417
0.5746 Remote Similarity NPC316598
0.5736 Remote Similarity NPC472676
0.5736 Remote Similarity NPC472688
0.5735 Remote Similarity NPC320447
0.5732 Remote Similarity NPC302276
0.5732 Remote Similarity NPC180770
0.5725 Remote Similarity NPC55462
0.5725 Remote Similarity NPC154601
0.5714 Remote Similarity NPC249954
0.5714 Remote Similarity NPC315915
0.5714 Remote Similarity NPC40687
0.5714 Remote Similarity NPC469515
0.5714 Remote Similarity NPC175614
0.5705 Remote Similarity NPC469494
0.5704 Remote Similarity NPC154072
0.5704 Remote Similarity NPC475970
0.5696 Remote Similarity NPC82931
0.5696 Remote Similarity NPC210729
0.5696 Remote Similarity NPC172365
0.5692 Remote Similarity NPC230332
0.5691 Remote Similarity NPC469517
0.5687 Remote Similarity NPC475892
0.5687 Remote Similarity NPC141669
0.5686 Remote Similarity NPC475472
0.5686 Remote Similarity NPC139585
0.5686 Remote Similarity NPC472413
0.5683 Remote Similarity NPC473284
0.5682 Remote Similarity NPC8993
0.5682 Remote Similarity NPC196227
0.5682 Remote Similarity NPC103527
0.5677 Remote Similarity NPC42423
0.5672 Remote Similarity NPC273269
0.5669 Remote Similarity NPC187529
0.5669 Remote Similarity NPC476558
0.5662 Remote Similarity NPC224172
0.5662 Remote Similarity NPC476223
0.5662 Remote Similarity NPC224720
0.5662 Remote Similarity NPC476240
0.5662 Remote Similarity NPC472637
0.5662 Remote Similarity NPC316250
0.566 Remote Similarity NPC162910
0.5659 Remote Similarity NPC229612
0.5659 Remote Similarity NPC7280
0.5659 Remote Similarity NPC104560
0.5655 Remote Similarity NPC271621
0.5655 Remote Similarity NPC59751
0.5655 Remote Similarity NPC474518
0.5655 Remote Similarity NPC27413
0.5652 Remote Similarity NPC470073
0.5652 Remote Similarity NPC239162
0.5649 Remote Similarity NPC116726
0.5649 Remote Similarity NPC314361
0.5649 Remote Similarity NPC475806
0.5649 Remote Similarity NPC119794
0.5649 Remote Similarity NPC73829
0.5649 Remote Similarity NPC472975
0.5646 Remote Similarity NPC473145
0.5646 Remote Similarity NPC31641
0.5646 Remote Similarity NPC476815
0.5645 Remote Similarity NPC148685
0.5645 Remote Similarity NPC104120
0.5645 Remote Similarity NPC157895

  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 NPC96425 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
0.5957 Remote Similarity NPD5167 Approved
0.5874 Remote Similarity NPD7500 Approved
0.5857 Remote Similarity NPD5217 Approved
0.5857 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5857 Remote Similarity NPD5216 Approved
0.5769 Remote Similarity NPD6333 Approved
0.5769 Remote Similarity NPD6334 Approved
0.5755 Remote Similarity NPD5168 Approved
0.5685 Remote Similarity NPD7101 Approved
0.5676 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5676 Remote Similarity NPD7623 Phase 3
0.5674 Remote Similarity NPD6420 Discontinued
0.5674 Remote Similarity NPD5169 Approved
0.5634 Remote Similarity NPD5215 Approved
0.5634 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5634 Remote Similarity NPD5127 Approved
0.5621 Remote Similarity NPD6914 Discontinued
0.5608 Remote Similarity NPD7739 Clinical (unspecified phase)

  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