Structure

Physi-Chem Properties

Molecular Weight:  487.19
Volume:  478.735
LogP:  3.801
LogD:  2.852
LogS:  -3.79
# Rotatable Bonds:  11
TPSA:  95.86
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.246
Synthetic Accessibility Score:  5.65
Fsp3:  0.667
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:  -4.725
MDCK Permeability:  2.7212514396524057e-05
Pgp-inhibitor:  0.981
Pgp-substrate:  0.594
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.962
Plasma Protein Binding (PPB):  94.13312530517578%
Volume Distribution (VD):  1.479
Pgp-substrate:  4.625650405883789%

ADMET: Metabolism

CYP1A2-inhibitor:  0.03
CYP1A2-substrate:  0.647
CYP2C19-inhibitor:  0.517
CYP2C19-substrate:  0.666
CYP2C9-inhibitor:  0.538
CYP2C9-substrate:  0.093
CYP2D6-inhibitor:  0.089
CYP2D6-substrate:  0.293
CYP3A4-inhibitor:  0.871
CYP3A4-substrate:  0.406

ADMET: Excretion

Clearance (CL):  2.609
Half-life (T1/2):  0.528

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.635
Drug-inuced Liver Injury (DILI):  0.039
AMES Toxicity:  0.244
Rat Oral Acute Toxicity:  0.456
Maximum Recommended Daily Dose:  0.875
Skin Sensitization:  0.938
Carcinogencity:  0.724
Eye Corrosion:  0.005
Eye Irritation:  0.019
Respiratory Toxicity:  0.982

Download Data

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

  Natural Product: NPC77481

Natural Product ID:  NPC77481
Common Name*:   Gymnastatin Q
IUPAC Name:   (2E,4E,6R)-N-[(1S,5S,6R,7S,9S)-3,5-dichloro-1,6-dihydroxy-9-methoxy-4-oxo-7-bicyclo[3.3.1]non-2-enyl]-4,6-dimethyldodeca-2,4-dienamide
Synonyms:   Gymnastatin Q
Standard InCHIKey:  MZPLGIXULRXDSO-HKYLIPGXSA-N
Standard InCHI:  InChI=1S/C24H35Cl2NO5/c1-5-6-7-8-9-15(2)12-16(3)10-11-19(28)27-18-14-23(31)13-17(25)20(29)24(26,21(18)30)22(23)32-4/h10-13,15,18,21-22,30-31H,5-9,14H2,1-4H3,(H,27,28)/b11-10+,16-12+/t15-,18+,21-,22+,23-,24+/m1/s1
SMILES:  CCCCCC[C@H](/C=C(/C=C/C(=N[C@H]1C[C@]2(O)C=C(C(=O)[C@]([C@@H]1O)([C@H]2OC)Cl)Cl)O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL254378
PubChem CID:   24854448
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 = 1.7 ug ml-1 PMID[466482]
NPT168 Cell Line P388 Mus musculus GI50 = 15488.17 nM PMID[466482]
NPT2398 Cell Line MKN-7 Homo sapiens GI50 = 6760.83 nM PMID[466482]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 3388.44 nM PMID[466482]

☑ 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 NPC77481 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
1.0 High Similarity NPC233770
0.9023 High Similarity NPC96425
0.8811 High Similarity NPC475837
0.7826 Intermediate Similarity NPC16709
0.7801 Intermediate Similarity NPC164476
0.7801 Intermediate Similarity NPC121601
0.7801 Intermediate Similarity NPC471471
0.7708 Intermediate Similarity NPC78189
0.7551 Intermediate Similarity NPC230889
0.702 Intermediate Similarity NPC472430
0.6923 Remote Similarity NPC323532
0.6918 Remote Similarity NPC204639
0.6842 Remote Similarity NPC472428
0.6735 Remote Similarity NPC280498
0.66 Remote Similarity NPC204556
0.6525 Remote Similarity NPC133729
0.6503 Remote Similarity NPC298005
0.6503 Remote Similarity NPC36463
0.6446 Remote Similarity NPC113620
0.6446 Remote Similarity NPC100612
0.6446 Remote Similarity NPC475599
0.6446 Remote Similarity NPC174336
0.6446 Remote Similarity NPC187497
0.6429 Remote Similarity NPC472615
0.6386 Remote Similarity NPC265699
0.6386 Remote Similarity NPC475527
0.6358 Remote Similarity NPC214821
0.6358 Remote Similarity NPC298067
0.634 Remote Similarity NPC477793
0.634 Remote Similarity NPC329919
0.6338 Remote Similarity NPC140251
0.6338 Remote Similarity NPC307903
0.6296 Remote Similarity NPC141669
0.628 Remote Similarity NPC244380
0.628 Remote Similarity NPC61717
0.6266 Remote Similarity NPC145899
0.625 Remote Similarity NPC469494
0.6242 Remote Similarity NPC76999
0.6241 Remote Similarity NPC472616
0.6218 Remote Similarity NPC139585
0.6216 Remote Similarity NPC476190
0.6216 Remote Similarity NPC316325
0.6203 Remote Similarity NPC75318
0.6196 Remote Similarity NPC298469
0.6196 Remote Similarity NPC193579
0.6188 Remote Similarity NPC476558
0.6188 Remote Similarity NPC200788
0.6188 Remote Similarity NPC243680
0.6181 Remote Similarity NPC474725
0.6178 Remote Similarity NPC314361
0.6169 Remote Similarity NPC478207
0.6164 Remote Similarity NPC476269
0.6164 Remote Similarity NPC469865
0.6159 Remote Similarity NPC469515
0.6149 Remote Similarity NPC180770
0.6149 Remote Similarity NPC302276
0.6122 Remote Similarity NPC122404
0.6118 Remote Similarity NPC188222
0.6118 Remote Similarity NPC310035
0.6118 Remote Similarity NPC282003
0.6115 Remote Similarity NPC475472
0.6115 Remote Similarity NPC189393
0.6115 Remote Similarity NPC90814
0.6111 Remote Similarity NPC172365
0.6111 Remote Similarity NPC82931
0.6111 Remote Similarity NPC210729
0.6098 Remote Similarity NPC160222
0.6098 Remote Similarity NPC193753
0.6098 Remote Similarity NPC475892
0.6081 Remote Similarity NPC80650
0.6078 Remote Similarity NPC303006
0.6076 Remote Similarity NPC73829
0.6076 Remote Similarity NPC119794
0.6074 Remote Similarity NPC162910
0.6067 Remote Similarity NPC9714
0.6062 Remote Similarity NPC130447
0.6056 Remote Similarity NPC474563
0.6054 Remote Similarity NPC7797
0.6049 Remote Similarity NPC208725
0.6042 Remote Similarity NPC475800
0.604 Remote Similarity NPC30196
0.6037 Remote Similarity NPC475152
0.6037 Remote Similarity NPC475394
0.6037 Remote Similarity NPC475584
0.6027 Remote Similarity NPC476290
0.6026 Remote Similarity NPC477352
0.6013 Remote Similarity NPC470185
0.6 Remote Similarity NPC216335
0.6 Remote Similarity NPC27999
0.6 Remote Similarity NPC147707
0.6 Remote Similarity NPC477116
0.6 Remote Similarity NPC102843
0.6 Remote Similarity NPC6531
0.6 Remote Similarity NPC235772
0.6 Remote Similarity NPC280941
0.5988 Remote Similarity NPC473233
0.5987 Remote Similarity NPC477143
0.5987 Remote Similarity NPC475885
0.5987 Remote Similarity NPC477140
0.5986 Remote Similarity NPC29501
0.5974 Remote Similarity NPC314629
0.5974 Remote Similarity NPC477995
0.5972 Remote Similarity NPC128828
0.5972 Remote Similarity NPC472433
0.5963 Remote Similarity NPC243902
0.5962 Remote Similarity NPC287903
0.5962 Remote Similarity NPC471940
0.5962 Remote Similarity NPC156797
0.596 Remote Similarity NPC251310
0.5959 Remote Similarity NPC473578
0.5959 Remote Similarity NPC87335
0.5952 Remote Similarity NPC31171
0.5952 Remote Similarity NPC237240
0.5951 Remote Similarity NPC265908
0.5944 Remote Similarity NPC469980
0.5944 Remote Similarity NPC118902
0.5944 Remote Similarity NPC104161
0.5941 Remote Similarity NPC201692
0.5938 Remote Similarity NPC477072
0.5935 Remote Similarity NPC314451
0.5935 Remote Similarity NPC313333
0.5935 Remote Similarity NPC313342
0.5935 Remote Similarity NPC314512
0.5931 Remote Similarity NPC313272
0.5931 Remote Similarity NPC266514
0.5931 Remote Similarity NPC319537
0.5931 Remote Similarity NPC251330
0.5926 Remote Similarity NPC246209
0.5921 Remote Similarity NPC236918
0.5921 Remote Similarity NPC156745
0.5918 Remote Similarity NPC92829
0.5918 Remote Similarity NPC122926
0.5918 Remote Similarity NPC46764
0.5918 Remote Similarity NPC113012
0.5915 Remote Similarity NPC473396
0.5912 Remote Similarity NPC142838
0.5912 Remote Similarity NPC477996
0.5909 Remote Similarity NPC20035
0.5904 Remote Similarity NPC69176
0.5904 Remote Similarity NPC284625
0.5897 Remote Similarity NPC471939
0.5897 Remote Similarity NPC293112
0.5897 Remote Similarity NPC225049
0.5894 Remote Similarity NPC474518
0.589 Remote Similarity NPC113325
0.589 Remote Similarity NPC279045
0.589 Remote Similarity NPC475150
0.5886 Remote Similarity NPC316205
0.5886 Remote Similarity NPC315387
0.5882 Remote Similarity NPC472759
0.5882 Remote Similarity NPC478051
0.5882 Remote Similarity NPC329080
0.5879 Remote Similarity NPC120667
0.5879 Remote Similarity NPC278272
0.5878 Remote Similarity NPC476023
0.5878 Remote Similarity NPC170375
0.5875 Remote Similarity NPC476111
0.5874 Remote Similarity NPC128501
0.5874 Remote Similarity NPC39996
0.5867 Remote Similarity NPC472400
0.5867 Remote Similarity NPC24462
0.5867 Remote Similarity NPC471645
0.5862 Remote Similarity NPC154601
0.5862 Remote Similarity NPC271269
0.586 Remote Similarity NPC475649
0.5855 Remote Similarity NPC234522
0.5855 Remote Similarity NPC284707
0.5854 Remote Similarity NPC175870
0.5849 Remote Similarity NPC475314
0.5849 Remote Similarity NPC477189
0.5849 Remote Similarity NPC475606
0.5849 Remote Similarity NPC251564
0.5849 Remote Similarity NPC471691
0.5844 Remote Similarity NPC156379
0.5844 Remote Similarity NPC475383
0.5844 Remote Similarity NPC67569
0.5839 Remote Similarity NPC476801
0.5839 Remote Similarity NPC261750
0.5839 Remote Similarity NPC1111
0.5839 Remote Similarity NPC472002
0.5833 Remote Similarity NPC473919
0.5833 Remote Similarity NPC473144
0.5833 Remote Similarity NPC172154
0.5833 Remote Similarity NPC473709
0.5833 Remote Similarity NPC297281
0.5833 Remote Similarity NPC81736
0.5828 Remote Similarity NPC228511
0.5824 Remote Similarity NPC173934
0.5813 Remote Similarity NPC316401
0.5813 Remote Similarity NPC473485
0.5813 Remote Similarity NPC474508
0.5813 Remote Similarity NPC471692
0.5812 Remote Similarity NPC475336
0.5812 Remote Similarity NPC471754
0.5812 Remote Similarity NPC453583
0.5812 Remote Similarity NPC473300
0.5812 Remote Similarity NPC317882
0.5811 Remote Similarity NPC474567
0.5808 Remote Similarity NPC111586
0.5808 Remote Similarity NPC108852

  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 NPC77481 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
0.6216 Remote Similarity NPD7500 Approved
0.6027 Remote Similarity NPD6421 Discontinued
0.5952 Remote Similarity NPD7274 Clinical (unspecified phase)
0.5935 Remote Similarity NPD8341 Approved
0.5935 Remote Similarity NPD8342 Approved
0.5935 Remote Similarity NPD8299 Approved
0.5935 Remote Similarity NPD8340 Approved
0.5878 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5878 Remote Similarity NPD7116 Clinical (unspecified phase)
0.586 Remote Similarity NPD8074 Phase 3
0.5855 Remote Similarity NPD7641 Discontinued
0.5796 Remote Similarity NPD8451 Approved
0.5793 Remote Similarity NPD6334 Approved
0.5793 Remote Similarity NPD6333 Approved
0.5769 Remote Similarity NPD7829 Approved
0.5769 Remote Similarity NPD7642 Approved
0.5769 Remote Similarity NPD7830 Approved
0.5759 Remote Similarity NPD8448 Approved
0.575 Remote Similarity NPD8392 Approved
0.575 Remote Similarity NPD8390 Approved
0.575 Remote Similarity NPD8391 Approved
0.5705 Remote Similarity NPD7623 Phase 3
0.5705 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5696 Remote Similarity NPD8273 Phase 1
0.5689 Remote Similarity NPD8384 Approved
0.5684 Remote Similarity NPD5036 Approved
0.5679 Remote Similarity NPD8338 Approved
0.5677 Remote Similarity NPD8361 Approved
0.5677 Remote Similarity NPD8360 Approved
0.5671 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5667 Remote Similarity NPD1719 Phase 1
0.5663 Remote Similarity NPD8485 Approved
0.5661 Remote Similarity NPD5035 Approved
0.5654 Remote Similarity NPD5037 Approved
0.5654 Remote Similarity NPD5038 Approved
0.5652 Remote Similarity NPD6914 Discontinued
0.5646 Remote Similarity NPD5357 Phase 1
0.5641 Remote Similarity NPD6921 Approved
0.5638 Remote Similarity NPD8368 Discontinued
0.5632 Remote Similarity NPD8407 Phase 2
0.561 Remote Similarity NPD8415 Approved
0.5606 Remote Similarity NPD5544 Approved
0.56 Remote Similarity NPD4386 Approved
0.56 Remote Similarity NPD4387 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