Structure

Physi-Chem Properties

Molecular Weight:  469.22
Volume:  466.394
LogP:  3.158
LogD:  2.773
LogS:  -3.451
# Rotatable Bonds:  11
TPSA:  108.39
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.196
Synthetic Accessibility Score:  5.867
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.711
MDCK Permeability:  2.906908412114717e-05
Pgp-inhibitor:  0.989
Pgp-substrate:  0.935
Human Intestinal Absorption (HIA):  0.207
20% Bioavailability (F20%):  0.396
30% Bioavailability (F30%):  0.064

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.362
Plasma Protein Binding (PPB):  93.96587371826172%
Volume Distribution (VD):  1.742
Pgp-substrate:  6.0975022315979%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.482
CYP2C19-inhibitor:  0.126
CYP2C19-substrate:  0.639
CYP2C9-inhibitor:  0.166
CYP2C9-substrate:  0.063
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.295
CYP3A4-inhibitor:  0.351
CYP3A4-substrate:  0.326

ADMET: Excretion

Clearance (CL):  7.439
Half-life (T1/2):  0.512

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.161
Drug-inuced Liver Injury (DILI):  0.046
AMES Toxicity:  0.188
Rat Oral Acute Toxicity:  0.578
Maximum Recommended Daily Dose:  0.726
Skin Sensitization:  0.828
Carcinogencity:  0.863
Eye Corrosion:  0.073
Eye Irritation:  0.062
Respiratory Toxicity:  0.989

Download Data

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

  Natural Product: NPC475837

Natural Product ID:  NPC475837
Common Name*:   Gymnastatin G
IUPAC Name:   n.a.
Synonyms:   Gymnastatin G
Standard InCHIKey:  NLDGIHUFOADNER-REUAAKEVSA-N
Standard InCHI:  InChI=1S/C24H36ClNO6/c1-5-6-7-8-9-14(2)12-15(3)10-11-17(27)26-16-13-23(30)21-18(32-21)20(29)24(25,19(16)28)22(23)31-4/h10-12,14,16,18-19,21-22,28,30H,5-9,13H2,1-4H3,(H,26,27)/b11-10+,15-12+/t14-,16+,18+,19+,21+,22+,23+,24-/m1/s1
SMILES:  CCCCCC[C@H](/C=C(/C=C/C(=N[C@H]1C[C@]2(O)[C@H]3O[C@H]3C(=O)[C@]([C@H]1O)([C@H]2OC)Cl)O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL517147
PubChem CID:   44559132
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001729] Oxepanes

*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 = 0.03 ug ml-1 PMID[455990]

☑ 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 NPC475837 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
0.8811 High Similarity NPC77481
0.8811 High Similarity NPC233770
0.8676 High Similarity NPC121601
0.8676 High Similarity NPC471471
0.8676 High Similarity NPC164476
0.8028 Intermediate Similarity NPC96425
0.7808 Intermediate Similarity NPC472430
0.7619 Intermediate Similarity NPC472428
0.7413 Intermediate Similarity NPC280498
0.7133 Intermediate Similarity NPC323532
0.6939 Remote Similarity NPC16709
0.6863 Remote Similarity NPC78189
0.6736 Remote Similarity NPC80650
0.6731 Remote Similarity NPC230889
0.6667 Remote Similarity NPC204639
0.6516 Remote Similarity NPC470185
0.6447 Remote Similarity NPC469494
0.6429 Remote Similarity NPC329919
0.6429 Remote Similarity NPC477793
0.6358 Remote Similarity NPC469515
0.6301 Remote Similarity NPC476023
0.6258 Remote Similarity NPC204556
0.625 Remote Similarity NPC145899
0.6226 Remote Similarity NPC76999
0.6216 Remote Similarity NPC477266
0.6209 Remote Similarity NPC188222
0.6209 Remote Similarity NPC310035
0.6209 Remote Similarity NPC282003
0.62 Remote Similarity NPC147707
0.6194 Remote Similarity NPC225049
0.619 Remote Similarity NPC298005
0.619 Remote Similarity NPC36463
0.6188 Remote Similarity NPC75318
0.6182 Remote Similarity NPC193753
0.6182 Remote Similarity NPC160222
0.6173 Remote Similarity NPC200788
0.6173 Remote Similarity NPC243680
0.6169 Remote Similarity NPC303006
0.6164 Remote Similarity NPC87335
0.6164 Remote Similarity NPC474725
0.6154 Remote Similarity NPC471940
0.6145 Remote Similarity NPC214821
0.6145 Remote Similarity NPC298067
0.614 Remote Similarity NPC187497
0.614 Remote Similarity NPC100612
0.614 Remote Similarity NPC174336
0.614 Remote Similarity NPC475599
0.614 Remote Similarity NPC113620
0.6133 Remote Similarity NPC179626
0.6107 Remote Similarity NPC122404
0.6101 Remote Similarity NPC475472
0.6098 Remote Similarity NPC172365
0.6098 Remote Similarity NPC82931
0.6098 Remote Similarity NPC210729
0.6096 Remote Similarity NPC70235
0.6093 Remote Similarity NPC27999
0.6093 Remote Similarity NPC477116
0.609 Remote Similarity NPC471939
0.609 Remote Similarity NPC470973
0.6087 Remote Similarity NPC99864
0.6084 Remote Similarity NPC475892
0.6082 Remote Similarity NPC475527
0.6082 Remote Similarity NPC265699
0.6081 Remote Similarity NPC29501
0.6078 Remote Similarity NPC475003
0.6071 Remote Similarity NPC61717
0.6071 Remote Similarity NPC279722
0.6071 Remote Similarity NPC244380
0.6062 Remote Similarity NPC119794
0.6062 Remote Similarity NPC314361
0.6062 Remote Similarity NPC73829
0.6053 Remote Similarity NPC251310
0.6047 Remote Similarity NPC4108
0.6038 Remote Similarity NPC477189
0.6038 Remote Similarity NPC475314
0.6038 Remote Similarity NPC251564
0.6038 Remote Similarity NPC475606
0.6028 Remote Similarity NPC236176
0.6027 Remote Similarity NPC475800
0.6026 Remote Similarity NPC473919
0.6026 Remote Similarity NPC313342
0.6026 Remote Similarity NPC313333
0.6026 Remote Similarity NPC314451
0.6026 Remote Similarity NPC473709
0.6026 Remote Similarity NPC314512
0.6025 Remote Similarity NPC120420
0.6024 Remote Similarity NPC475152
0.6024 Remote Similarity NPC475584
0.6024 Remote Similarity NPC475394
0.6013 Remote Similarity NPC470186
0.6 Remote Similarity NPC473485
0.6 Remote Similarity NPC474508
0.6 Remote Similarity NPC139585
0.5988 Remote Similarity NPC235772
0.5988 Remote Similarity NPC280941
0.5988 Remote Similarity NPC141669
0.5987 Remote Similarity NPC470775
0.5987 Remote Similarity NPC176513
0.5986 Remote Similarity NPC102843
0.5976 Remote Similarity NPC476558
0.5974 Remote Similarity NPC478051
0.5962 Remote Similarity NPC477995
0.5962 Remote Similarity NPC473802
0.5951 Remote Similarity NPC243902
0.5949 Remote Similarity NPC478207
0.5948 Remote Similarity NPC470776
0.5939 Remote Similarity NPC175870
0.5931 Remote Similarity NPC215988
0.5931 Remote Similarity NPC469980
0.5931 Remote Similarity NPC118902
0.5931 Remote Similarity NPC104161
0.5926 Remote Similarity NPC475500
0.5926 Remote Similarity NPC223356
0.5926 Remote Similarity NPC100017
0.5926 Remote Similarity NPC182266
0.5926 Remote Similarity NPC475154
0.5926 Remote Similarity NPC471136
0.5926 Remote Similarity NPC473548
0.5926 Remote Similarity NPC471137
0.5924 Remote Similarity NPC476729
0.5921 Remote Similarity NPC474734
0.5918 Remote Similarity NPC266514
0.5918 Remote Similarity NPC474716
0.5912 Remote Similarity NPC476091
0.5912 Remote Similarity NPC476078
0.5912 Remote Similarity NPC477352
0.5906 Remote Similarity NPC46764
0.5906 Remote Similarity NPC92829
0.5904 Remote Similarity NPC473396
0.5901 Remote Similarity NPC477996
0.5901 Remote Similarity NPC471692
0.5901 Remote Similarity NPC90814
0.5901 Remote Similarity NPC189393
0.5894 Remote Similarity NPC317210
0.5893 Remote Similarity NPC193579
0.5893 Remote Similarity NPC298469
0.5886 Remote Similarity NPC293112
0.5882 Remote Similarity NPC296822
0.5882 Remote Similarity NPC476190
0.5882 Remote Similarity NPC476713
0.5882 Remote Similarity NPC476712
0.5878 Remote Similarity NPC289702
0.5878 Remote Similarity NPC208461
0.5878 Remote Similarity NPC475150
0.5875 Remote Similarity NPC162495
0.5871 Remote Similarity NPC477143
0.5871 Remote Similarity NPC477140
0.5867 Remote Similarity NPC170375
0.5867 Remote Similarity NPC157476
0.5867 Remote Similarity NPC317107
0.5862 Remote Similarity NPC39996
0.5862 Remote Similarity NPC128501
0.586 Remote Similarity NPC265557
0.586 Remote Similarity NPC67251
0.586 Remote Similarity NPC105926
0.586 Remote Similarity NPC91693
0.586 Remote Similarity NPC18945
0.5855 Remote Similarity NPC476813
0.5855 Remote Similarity NPC117712
0.5855 Remote Similarity NPC476814
0.5855 Remote Similarity NPC33372
0.5855 Remote Similarity NPC67246
0.5855 Remote Similarity NPC73314
0.5854 Remote Similarity NPC68282
0.5854 Remote Similarity NPC130447
0.5849 Remote Similarity NPC314282
0.5844 Remote Similarity NPC284707
0.5844 Remote Similarity NPC200412
0.5844 Remote Similarity NPC156336
0.5844 Remote Similarity NPC478206
0.5844 Remote Similarity NPC108581
0.5844 Remote Similarity NPC478205
0.5844 Remote Similarity NPC120599
0.5844 Remote Similarity NPC240509
0.5843 Remote Similarity NPC302276
0.5843 Remote Similarity NPC265908
0.5843 Remote Similarity NPC180770
0.5839 Remote Similarity NPC475389
0.5839 Remote Similarity NPC133729
0.5839 Remote Similarity NPC471691
0.5839 Remote Similarity NPC473838
0.5838 Remote Similarity NPC201692
0.5833 Remote Similarity NPC472401
0.5833 Remote Similarity NPC102822
0.5833 Remote Similarity NPC269713
0.5833 Remote Similarity NPC475383
0.5833 Remote Similarity NPC23963
0.5833 Remote Similarity NPC470779
0.5833 Remote Similarity NPC477046
0.5833 Remote Similarity NPC156379
0.5828 Remote Similarity NPC473877
0.5828 Remote Similarity NPC469865
0.5828 Remote Similarity NPC476269
0.5828 Remote Similarity NPC317687
0.5823 Remote Similarity NPC172154
0.5823 Remote Similarity NPC81736
0.5817 Remote Similarity NPC477509
0.5817 Remote Similarity NPC476710
0.5817 Remote Similarity NPC474333
0.5817 Remote Similarity NPC476711

  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 NPC475837 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
0.6159 Remote Similarity NPD8384 Approved
0.6149 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6144 Remote Similarity NPD6921 Approved
0.6087 Remote Similarity NPD8415 Approved
0.6026 Remote Similarity NPD8341 Approved
0.6026 Remote Similarity NPD8340 Approved
0.6026 Remote Similarity NPD8342 Approved
0.6026 Remote Similarity NPD8299 Approved
0.5976 Remote Similarity NPD6333 Approved
0.5976 Remote Similarity NPD6334 Approved
0.5906 Remote Similarity NPD6421 Discontinued
0.5886 Remote Similarity NPD8451 Approved
0.5878 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5867 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5849 Remote Similarity NPD8448 Approved
0.5849 Remote Similarity NPD8074 Phase 3
0.5839 Remote Similarity NPD8392 Approved
0.5839 Remote Similarity NPD8391 Approved
0.5839 Remote Similarity NPD8390 Approved
0.5786 Remote Similarity NPD6336 Discontinued
0.5786 Remote Similarity NPD8273 Phase 1
0.5759 Remote Similarity NPD7830 Approved
0.5759 Remote Similarity NPD7642 Approved
0.5759 Remote Similarity NPD7829 Approved
0.5743 Remote Similarity NPD5357 Phase 1
0.5736 Remote Similarity NPD8485 Approved
0.5714 Remote Similarity NPD8368 Discontinued
0.5707 Remote Similarity NPD8407 Phase 2
0.567 Remote Similarity NPD8360 Approved
0.567 Remote Similarity NPD8435 Approved
0.567 Remote Similarity NPD8361 Approved
0.5665 Remote Similarity NPD7274 Clinical (unspecified phase)
0.565 Remote Similarity NPD8486 Clinical (unspecified phase)
0.5646 Remote Similarity NPD3653 Clinical (unspecified phase)
0.5641 Remote Similarity NPD7641 Discontinued
0.5633 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5633 Remote Similarity NPD8444 Approved
0.5617 Remote Similarity NPD6033 Approved
0.5605 Remote Similarity NPD7101 Approved
0.56 Remote Similarity NPD5544 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