Structure

Physi-Chem Properties

Molecular Weight:  455.16
Volume:  450.012
LogP:  4.145
LogD:  3.21
LogS:  -3.92
# Rotatable Bonds:  10
TPSA:  75.63
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.377
Synthetic Accessibility Score:  4.773
Fsp3:  0.565
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.712
MDCK Permeability:  1.79118706000736e-05
Pgp-inhibitor:  0.174
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.954
Plasma Protein Binding (PPB):  94.62738037109375%
Volume Distribution (VD):  2.478
Pgp-substrate:  4.985755920410156%

ADMET: Metabolism

CYP1A2-inhibitor:  0.062
CYP1A2-substrate:  0.627
CYP2C19-inhibitor:  0.943
CYP2C19-substrate:  0.755
CYP2C9-inhibitor:  0.912
CYP2C9-substrate:  0.752
CYP2D6-inhibitor:  0.739
CYP2D6-substrate:  0.692
CYP3A4-inhibitor:  0.899
CYP3A4-substrate:  0.28

ADMET: Excretion

Clearance (CL):  1.662
Half-life (T1/2):  0.737

ADMET: Toxicity

hERG Blockers:  0.056
Human Hepatotoxicity (H-HT):  0.848
Drug-inuced Liver Injury (DILI):  0.036
AMES Toxicity:  0.406
Rat Oral Acute Toxicity:  0.693
Maximum Recommended Daily Dose:  0.91
Skin Sensitization:  0.943
Carcinogencity:  0.897
Eye Corrosion:  0.003
Eye Irritation:  0.022
Respiratory Toxicity:  0.977

Download Data

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

  Natural Product: NPC472433

Natural Product ID:  NPC472433
Common Name*:   Gymnastatin A
IUPAC Name:   (2E,4E,6R)-N-[(3S)-7,9-dichloro-2-hydroxy-8-oxo-1-oxaspiro[4.5]deca-6,9-dien-3-yl]-4,6-dimethyldodeca-2,4-dienamide
Synonyms:  
Standard InCHIKey:  NGXMXBNROHVABT-SFZUPXHJSA-N
Standard InCHI:  InChI=1S/C23H31Cl2NO4/c1-4-5-6-7-8-15(2)11-16(3)9-10-20(27)26-19-14-23(30-22(19)29)12-17(24)21(28)18(25)13-23/h9-13,15,19,22,29H,4-8,14H2,1-3H3,(H,26,27)/b10-9+,16-11+/t15-,19+,22?/m1/s1
SMILES:  CCCCCCC(C)C=C(C)C=CC(=O)NC1CC2(C=C(C(=O)C(=C2)Cl)Cl)OC1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3402612
PubChem CID:   11798048
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000331] Fatty amides
          • [CHEMONTID:0001096] N-acyl amines

*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
NPT1864 Cell Line L5178Y Mus musculus IC50 = 640.0 nM PMID[481000]

☑ 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 NPC472433 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
0.776 Intermediate Similarity NPC230889
0.7244 Intermediate Similarity NPC78189
0.7073 Intermediate Similarity NPC16709
0.688 Remote Similarity NPC204639
0.6757 Remote Similarity NPC175614
0.6723 Remote Similarity NPC29501
0.6667 Remote Similarity NPC175531
0.6518 Remote Similarity NPC205546
0.6518 Remote Similarity NPC50902
0.6518 Remote Similarity NPC233273
0.65 Remote Similarity NPC122926
0.65 Remote Similarity NPC113012
0.6486 Remote Similarity NPC472613
0.6471 Remote Similarity NPC287572
0.6471 Remote Similarity NPC471636
0.6439 Remote Similarity NPC96425
0.6429 Remote Similarity NPC116930
0.6429 Remote Similarity NPC471022
0.6408 Remote Similarity NPC326753
0.64 Remote Similarity NPC477555
0.6379 Remote Similarity NPC313234
0.6372 Remote Similarity NPC189764
0.6325 Remote Similarity NPC473289
0.6321 Remote Similarity NPC324170
0.632 Remote Similarity NPC477553
0.6316 Remote Similarity NPC45313
0.6316 Remote Similarity NPC8098
0.6316 Remote Similarity NPC183449
0.6316 Remote Similarity NPC197294
0.6303 Remote Similarity NPC135216
0.6303 Remote Similarity NPC201128
0.6303 Remote Similarity NPC101106
0.6281 Remote Similarity NPC474891
0.6281 Remote Similarity NPC24389
0.6271 Remote Similarity NPC55336
0.626 Remote Similarity NPC273215
0.626 Remote Similarity NPC268327
0.626 Remote Similarity NPC295444
0.625 Remote Similarity NPC472430
0.625 Remote Similarity NPC315426
0.623 Remote Similarity NPC127578
0.6204 Remote Similarity NPC471301
0.619 Remote Similarity NPC313911
0.619 Remote Similarity NPC314854
0.616 Remote Similarity NPC471645
0.614 Remote Similarity NPC157353
0.614 Remote Similarity NPC282088
0.614 Remote Similarity NPC23454
0.614 Remote Similarity NPC3568
0.614 Remote Similarity NPC158445
0.614 Remote Similarity NPC35269
0.614 Remote Similarity NPC54961
0.614 Remote Similarity NPC256570
0.614 Remote Similarity NPC192066
0.614 Remote Similarity NPC156782
0.614 Remote Similarity NPC70323
0.614 Remote Similarity NPC262312
0.614 Remote Similarity NPC17290
0.6129 Remote Similarity NPC279383
0.6121 Remote Similarity NPC167380
0.6121 Remote Similarity NPC4834
0.6116 Remote Similarity NPC250187
0.6111 Remote Similarity NPC106912
0.6111 Remote Similarity NPC263087
0.6111 Remote Similarity NPC27314
0.6111 Remote Similarity NPC2379
0.6111 Remote Similarity NPC31019
0.6102 Remote Similarity NPC474873
0.6087 Remote Similarity NPC13924
0.608 Remote Similarity NPC475988
0.6066 Remote Similarity NPC476034
0.6066 Remote Similarity NPC474969
0.6063 Remote Similarity NPC27413
0.6063 Remote Similarity NPC271621
0.6063 Remote Similarity NPC316325
0.6063 Remote Similarity NPC59751
0.6058 Remote Similarity NPC472428
0.605 Remote Similarity NPC477198
0.6036 Remote Similarity NPC472614
0.6019 Remote Similarity NPC323251
0.6019 Remote Similarity NPC471298
0.6018 Remote Similarity NPC209047
0.6018 Remote Similarity NPC242503
0.6018 Remote Similarity NPC43074
0.6018 Remote Similarity NPC139782
0.6018 Remote Similarity NPC477865
0.6018 Remote Similarity NPC74672
0.6018 Remote Similarity NPC477866
0.6 Remote Similarity NPC469865
0.6 Remote Similarity NPC474995
0.6 Remote Similarity NPC471300
0.6 Remote Similarity NPC473756
0.6 Remote Similarity NPC474860
0.5984 Remote Similarity NPC30196
0.5984 Remote Similarity NPC172197
0.5984 Remote Similarity NPC274293
0.5984 Remote Similarity NPC477554
0.5983 Remote Similarity NPC265662
0.5972 Remote Similarity NPC77481
0.5972 Remote Similarity NPC233770
0.597 Remote Similarity NPC329919
0.597 Remote Similarity NPC477793
0.5965 Remote Similarity NPC111567
0.5965 Remote Similarity NPC473950
0.5965 Remote Similarity NPC309898
0.5965 Remote Similarity NPC186840
0.5965 Remote Similarity NPC263545
0.5965 Remote Similarity NPC15851
0.5965 Remote Similarity NPC282705
0.5965 Remote Similarity NPC473604
0.5965 Remote Similarity NPC473581
0.5965 Remote Similarity NPC182632
0.5965 Remote Similarity NPC475125
0.5963 Remote Similarity NPC471297
0.595 Remote Similarity NPC75523
0.5946 Remote Similarity NPC211892
0.5943 Remote Similarity NPC4436
0.5941 Remote Similarity NPC45060
0.5941 Remote Similarity NPC280065
0.5938 Remote Similarity NPC6531
0.5932 Remote Similarity NPC203627
0.5923 Remote Similarity NPC473808
0.5922 Remote Similarity NPC314678
0.5917 Remote Similarity NPC469598
0.5913 Remote Similarity NPC475098
0.5913 Remote Similarity NPC189651
0.5913 Remote Similarity NPC469939
0.5913 Remote Similarity NPC242069
0.5913 Remote Similarity NPC59646
0.5909 Remote Similarity NPC471302
0.5909 Remote Similarity NPC470800
0.5909 Remote Similarity NPC126518
0.5909 Remote Similarity NPC161670
0.5902 Remote Similarity NPC154601
0.5902 Remote Similarity NPC475918
0.5902 Remote Similarity NPC472615
0.5897 Remote Similarity NPC121857
0.5897 Remote Similarity NPC475503
0.5896 Remote Similarity NPC262845
0.5896 Remote Similarity NPC473249
0.5896 Remote Similarity NPC68293
0.5893 Remote Similarity NPC313658
0.5893 Remote Similarity NPC475678
0.5893 Remote Similarity NPC316138
0.5891 Remote Similarity NPC9714
0.5887 Remote Similarity NPC298484
0.5878 Remote Similarity NPC469515
0.5878 Remote Similarity NPC315915
0.5872 Remote Similarity NPC471296
0.5868 Remote Similarity NPC474563
0.5865 Remote Similarity NPC470686
0.5865 Remote Similarity NPC469494
0.5862 Remote Similarity NPC475572
0.5862 Remote Similarity NPC470521
0.5862 Remote Similarity NPC470255
0.5859 Remote Similarity NPC7905
0.5859 Remote Similarity NPC477525
0.5859 Remote Similarity NPC315652
0.5856 Remote Similarity NPC163606
0.5856 Remote Similarity NPC474424
0.5847 Remote Similarity NPC476344
0.5847 Remote Similarity NPC98112
0.5847 Remote Similarity NPC475646
0.5842 Remote Similarity NPC249713
0.5841 Remote Similarity NPC60765
0.5841 Remote Similarity NPC316186
0.5839 Remote Similarity NPC475527
0.5833 Remote Similarity NPC469943
0.5827 Remote Similarity NPC5485
0.5826 Remote Similarity NPC472264
0.5826 Remote Similarity NPC118844
0.5826 Remote Similarity NPC61894
0.5826 Remote Similarity NPC72183
0.5826 Remote Similarity NPC475603
0.5826 Remote Similarity NPC299808
0.5826 Remote Similarity NPC110875
0.5825 Remote Similarity NPC316185
0.5822 Remote Similarity NPC61717
0.5822 Remote Similarity NPC244380
0.5818 Remote Similarity NPC16488
0.5816 Remote Similarity NPC471023
0.5814 Remote Similarity NPC65045
0.5814 Remote Similarity NPC476190
0.5812 Remote Similarity NPC150041
0.5806 Remote Similarity NPC140251
0.5806 Remote Similarity NPC307903
0.5806 Remote Similarity NPC470024
0.5804 Remote Similarity NPC311163
0.5804 Remote Similarity NPC315395
0.5804 Remote Similarity NPC316426
0.58 Remote Similarity NPC475599
0.58 Remote Similarity NPC174336
0.58 Remote Similarity NPC113620
0.58 Remote Similarity NPC187497
0.58 Remote Similarity NPC100612
0.5798 Remote Similarity NPC166770
0.5797 Remote Similarity NPC314361
0.5794 Remote Similarity NPC474833
0.5794 Remote Similarity NPC170375
0.5789 Remote Similarity NPC315783

  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 NPC472433 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
0.6311 Remote Similarity NPD7116 Clinical (unspecified phase)
0.6303 Remote Similarity NPD4211 Phase 1
0.6077 Remote Similarity NPD7623 Phase 3
0.6077 Remote Similarity NPD7624 Clinical (unspecified phase)
0.6063 Remote Similarity NPD7500 Approved
0.6018 Remote Similarity NPD8522 Clinical (unspecified phase)
0.6 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5938 Remote Similarity NPD7505 Discontinued
0.5909 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5896 Remote Similarity NPD7747 Phase 1
0.5896 Remote Similarity NPD7746 Phase 1
0.5891 Remote Similarity NPD7641 Discontinued
0.5794 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5789 Remote Similarity NPD7829 Approved
0.5789 Remote Similarity NPD7830 Approved
0.5789 Remote Similarity NPD7642 Approved
0.5766 Remote Similarity NPD6914 Discontinued
0.576 Remote Similarity NPD6413 Approved
0.5738 Remote Similarity NPD2258 Approved
0.5738 Remote Similarity NPD1407 Approved
0.5738 Remote Similarity NPD2259 Approved
0.5704 Remote Similarity NPD8451 Approved
0.5667 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5662 Remote Similarity NPD8448 Approved
0.5639 Remote Similarity NPD8444 Approved
0.563 Remote Similarity NPD8299 Approved
0.563 Remote Similarity NPD8342 Approved
0.563 Remote Similarity NPD8341 Approved
0.563 Remote Similarity NPD4228 Discovery
0.563 Remote Similarity NPD8340 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