Structure

Physi-Chem Properties

Molecular Weight:  487.19
Volume:  478.735
LogP:  4.024
LogD:  3.393
LogS:  -4.408
# Rotatable Bonds:  11
TPSA:  84.86
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.268
Synthetic Accessibility Score:  4.924
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.666
MDCK Permeability:  2.093283001158852e-05
Pgp-inhibitor:  0.982
Pgp-substrate:  0.087
Human Intestinal Absorption (HIA):  0.025
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.925
Plasma Protein Binding (PPB):  96.6148910522461%
Volume Distribution (VD):  2.64
Pgp-substrate:  2.665173292160034%

ADMET: Metabolism

CYP1A2-inhibitor:  0.019
CYP1A2-substrate:  0.431
CYP2C19-inhibitor:  0.443
CYP2C19-substrate:  0.742
CYP2C9-inhibitor:  0.59
CYP2C9-substrate:  0.064
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.327
CYP3A4-inhibitor:  0.908
CYP3A4-substrate:  0.278

ADMET: Excretion

Clearance (CL):  2.74
Half-life (T1/2):  0.558

ADMET: Toxicity

hERG Blockers:  0.037
Human Hepatotoxicity (H-HT):  0.244
Drug-inuced Liver Injury (DILI):  0.088
AMES Toxicity:  0.417
Rat Oral Acute Toxicity:  0.685
Maximum Recommended Daily Dose:  0.669
Skin Sensitization:  0.944
Carcinogencity:  0.706
Eye Corrosion:  0.011
Eye Irritation:  0.084
Respiratory Toxicity:  0.974

Download Data

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

  Natural Product: NPC78189

Natural Product ID:  NPC78189
Common Name*:   Dankastatin A
IUPAC Name:   (2E,4E,6R)-N-[(2S,3S,4aR,8S,8aS)-6,8-dichloro-4a-hydroxy-2-methoxy-7-oxo-3,4,8,8a-tetrahydro-2H-chromen-3-yl]-4,6-dimethyldodeca-2,4-dienamide
Synonyms:  
Standard InCHIKey:  BZCAAMLTKGWGQU-NVMAJLLBSA-N
Standard InCHI:  InChI=1S/C24H35Cl2NO5/c1-5-6-7-8-9-15(2)12-16(3)10-11-19(28)27-18-14-24(30)13-17(25)21(29)20(26)22(24)32-23(18)31-4/h10-13,15,18,20,22-23,30H,5-9,14H2,1-4H3,(H,27,28)/b11-10+,16-12+/t15-,18+,20-,22-,23+,24+/m1/s1
SMILES:  CCCCCC[C@H](/C=C(/C=C/C(=N[C@H]1C[C@@]2(O)C=C(Cl)C(=O)[C@H]([C@H]2O[C@@H]1OC)Cl)O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL255458
PubChem CID:   24854521
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans

*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 = 0.15 ug ml-1 PMID[449322]

☑ 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 NPC78189 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
0.9449 High Similarity NPC230889
0.9262 High Similarity NPC16709
0.8583 High Similarity NPC204639
0.7708 Intermediate Similarity NPC77481
0.7708 Intermediate Similarity NPC233770
0.7286 Intermediate Similarity NPC96425
0.7273 Intermediate Similarity NPC30196
0.7244 Intermediate Similarity NPC472433
0.7234 Intermediate Similarity NPC314361
0.7218 Intermediate Similarity NPC6531
0.7176 Intermediate Similarity NPC469865
0.7153 Intermediate Similarity NPC314629
0.7143 Intermediate Similarity NPC316205
0.7143 Intermediate Similarity NPC315387
0.7133 Intermediate Similarity NPC472428
0.7132 Intermediate Similarity NPC469515
0.7109 Intermediate Similarity NPC201128
0.7101 Intermediate Similarity NPC314451
0.7101 Intermediate Similarity NPC314512
0.7101 Intermediate Similarity NPC469494
0.7101 Intermediate Similarity NPC313333
0.7101 Intermediate Similarity NPC313342
0.709 Intermediate Similarity NPC316325
0.7083 Intermediate Similarity NPC472430
0.7045 Intermediate Similarity NPC261750
0.7045 Intermediate Similarity NPC1111
0.7045 Intermediate Similarity NPC60432
0.697 Remote Similarity NPC29501
0.695 Remote Similarity NPC477793
0.695 Remote Similarity NPC329919
0.6947 Remote Similarity NPC473578
0.6923 Remote Similarity NPC316401
0.6923 Remote Similarity NPC139585
0.6906 Remote Similarity NPC315783
0.6906 Remote Similarity NPC318445
0.6906 Remote Similarity NPC316133
0.6879 Remote Similarity NPC314282
0.687 Remote Similarity NPC475150
0.6863 Remote Similarity NPC475837
0.6846 Remote Similarity NPC472615
0.6818 Remote Similarity NPC133729
0.6795 Remote Similarity NPC475599
0.6795 Remote Similarity NPC174336
0.6795 Remote Similarity NPC187497
0.6795 Remote Similarity NPC113620
0.6795 Remote Similarity NPC100612
0.6739 Remote Similarity NPC314268
0.6739 Remote Similarity NPC313802
0.6739 Remote Similarity NPC477515
0.6739 Remote Similarity NPC67917
0.6731 Remote Similarity NPC475527
0.6731 Remote Similarity NPC265699
0.6711 Remote Similarity NPC214821
0.6711 Remote Similarity NPC298067
0.6645 Remote Similarity NPC298005
0.6645 Remote Similarity NPC36463
0.6643 Remote Similarity NPC204556
0.6641 Remote Similarity NPC472616
0.6623 Remote Similarity NPC244380
0.6623 Remote Similarity NPC61717
0.6622 Remote Similarity NPC145899
0.6615 Remote Similarity NPC477198
0.6614 Remote Similarity NPC175614
0.6599 Remote Similarity NPC76999
0.6591 Remote Similarity NPC475918
0.6569 Remote Similarity NPC471645
0.6562 Remote Similarity NPC266842
0.6554 Remote Similarity NPC75318
0.6536 Remote Similarity NPC141669
0.6536 Remote Similarity NPC193579
0.6536 Remote Similarity NPC298469
0.6533 Remote Similarity NPC243680
0.6533 Remote Similarity NPC200788
0.6493 Remote Similarity NPC140251
0.6493 Remote Similarity NPC307903
0.649 Remote Similarity NPC180770
0.649 Remote Similarity NPC302276
0.6484 Remote Similarity NPC197294
0.6484 Remote Similarity NPC8098
0.6484 Remote Similarity NPC45313
0.6484 Remote Similarity NPC183449
0.6479 Remote Similarity NPC469943
0.6471 Remote Similarity NPC12270
0.6463 Remote Similarity NPC475472
0.6452 Remote Similarity NPC316249
0.6447 Remote Similarity NPC82931
0.6447 Remote Similarity NPC210729
0.6447 Remote Similarity NPC172365
0.6444 Remote Similarity NPC24389
0.6438 Remote Similarity NPC471471
0.6438 Remote Similarity NPC164476
0.6438 Remote Similarity NPC121601
0.6434 Remote Similarity NPC280498
0.6429 Remote Similarity NPC475892
0.6429 Remote Similarity NPC477555
0.6419 Remote Similarity NPC73829
0.6419 Remote Similarity NPC119794
0.6418 Remote Similarity NPC315426
0.6408 Remote Similarity NPC315915
0.6405 Remote Similarity NPC162910
0.6391 Remote Similarity NPC74035
0.6364 Remote Similarity NPC475152
0.6364 Remote Similarity NPC803
0.6364 Remote Similarity NPC223834
0.6364 Remote Similarity NPC475394
0.6364 Remote Similarity NPC475584
0.6357 Remote Similarity NPC59751
0.6357 Remote Similarity NPC477553
0.6357 Remote Similarity NPC27413
0.6357 Remote Similarity NPC475503
0.6357 Remote Similarity NPC271621
0.6343 Remote Similarity NPC271269
0.6333 Remote Similarity NPC280941
0.6333 Remote Similarity NPC235772
0.6328 Remote Similarity NPC158445
0.6328 Remote Similarity NPC157353
0.6328 Remote Similarity NPC3568
0.6328 Remote Similarity NPC23454
0.6328 Remote Similarity NPC17290
0.6328 Remote Similarity NPC192066
0.6328 Remote Similarity NPC35269
0.6328 Remote Similarity NPC70323
0.6328 Remote Similarity NPC156782
0.6328 Remote Similarity NPC256570
0.6328 Remote Similarity NPC54961
0.6328 Remote Similarity NPC282088
0.6328 Remote Similarity NPC262312
0.6319 Remote Similarity NPC477995
0.6316 Remote Similarity NPC55336
0.6296 Remote Similarity NPC251330
0.6294 Remote Similarity NPC473228
0.6294 Remote Similarity NPC470829
0.6288 Remote Similarity NPC175531
0.6275 Remote Similarity NPC265908
0.6268 Remote Similarity NPC323532
0.6267 Remote Similarity NPC477072
0.6258 Remote Similarity NPC475266
0.6258 Remote Similarity NPC304299
0.6258 Remote Similarity NPC309450
0.6258 Remote Similarity NPC247776
0.6258 Remote Similarity NPC475278
0.625 Remote Similarity NPC472613
0.6242 Remote Similarity NPC476194
0.6241 Remote Similarity NPC475642
0.6241 Remote Similarity NPC476190
0.6232 Remote Similarity NPC170375
0.6224 Remote Similarity NPC473808
0.6222 Remote Similarity NPC154601
0.622 Remote Similarity NPC209047
0.622 Remote Similarity NPC139782
0.622 Remote Similarity NPC43074
0.622 Remote Similarity NPC74672
0.622 Remote Similarity NPC242503
0.6218 Remote Similarity NPC284625
0.6218 Remote Similarity NPC69176
0.6216 Remote Similarity NPC110294
0.6197 Remote Similarity NPC296361
0.6197 Remote Similarity NPC9714
0.6197 Remote Similarity NPC234522
0.6194 Remote Similarity NPC474563
0.619 Remote Similarity NPC473249
0.6187 Remote Similarity NPC7797
0.6187 Remote Similarity NPC476269
0.6183 Remote Similarity NPC475646
0.6183 Remote Similarity NPC474194
0.6183 Remote Similarity NPC245521
0.6183 Remote Similarity NPC278506
0.6181 Remote Similarity NPC475383
0.6181 Remote Similarity NPC156379
0.6172 Remote Similarity NPC475603
0.6172 Remote Similarity NPC473581
0.6172 Remote Similarity NPC111567
0.6172 Remote Similarity NPC475125
0.6172 Remote Similarity NPC186840
0.6172 Remote Similarity NPC309898
0.6172 Remote Similarity NPC472199
0.6172 Remote Similarity NPC263545
0.6172 Remote Similarity NPC15851
0.6172 Remote Similarity NPC182632
0.6172 Remote Similarity NPC472197
0.6172 Remote Similarity NPC61894
0.6172 Remote Similarity NPC473604
0.6172 Remote Similarity NPC473950
0.6172 Remote Similarity NPC282705
0.617 Remote Similarity NPC315652
0.617 Remote Similarity NPC7905
0.6163 Remote Similarity NPC278272
0.6163 Remote Similarity NPC120667
0.6159 Remote Similarity NPC113012
0.6159 Remote Similarity NPC89408
0.6159 Remote Similarity NPC122926
0.6154 Remote Similarity NPC71866
0.6154 Remote Similarity NPC108141
0.6143 Remote Similarity NPC5485
0.6136 Remote Similarity NPC187761
0.6136 Remote Similarity NPC83895
0.6136 Remote Similarity NPC475649
0.6136 Remote Similarity NPC203627
0.6133 Remote Similarity NPC477996
0.6127 Remote Similarity NPC23046

  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 NPC78189 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
0.7101 Intermediate Similarity NPD8342 Approved
0.7101 Intermediate Similarity NPD8340 Approved
0.7101 Intermediate Similarity NPD8341 Approved
0.7101 Intermediate Similarity NPD8299 Approved
0.709 Intermediate Similarity NPD7500 Approved
0.7037 Intermediate Similarity NPD7641 Discontinued
0.6929 Remote Similarity NPD8451 Approved
0.6906 Remote Similarity NPD7829 Approved
0.6906 Remote Similarity NPD7830 Approved
0.6906 Remote Similarity NPD7642 Approved
0.6879 Remote Similarity NPD8448 Approved
0.6853 Remote Similarity NPD8390 Approved
0.6853 Remote Similarity NPD8392 Approved
0.6853 Remote Similarity NPD8391 Approved
0.6736 Remote Similarity NPD6914 Discontinued
0.6643 Remote Similarity NPD8444 Approved
0.6593 Remote Similarity NPD7116 Clinical (unspecified phase)
0.6519 Remote Similarity NPD6421 Discontinued
0.6471 Remote Similarity NPD1719 Phase 1
0.6414 Remote Similarity NPD8074 Phase 3
0.6364 Remote Similarity NPD8080 Discontinued
0.6364 Remote Similarity NPD7624 Clinical (unspecified phase)
0.6364 Remote Similarity NPD7623 Phase 3
0.6299 Remote Similarity NPD8384 Approved
0.6294 Remote Similarity NPD7739 Clinical (unspecified phase)
0.626 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6241 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6232 Remote Similarity NPD7601 Clinical (unspecified phase)
0.622 Remote Similarity NPD8522 Clinical (unspecified phase)
0.619 Remote Similarity NPD7747 Phase 1
0.619 Remote Similarity NPD7746 Phase 1
0.6181 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6149 Remote Similarity NPD8336 Approved
0.6149 Remote Similarity NPD8337 Approved
0.6122 Remote Similarity NPD8273 Phase 1
0.6093 Remote Similarity NPD8338 Approved
0.6074 Remote Similarity NPD1407 Approved
0.6069 Remote Similarity NPD8516 Approved
0.6069 Remote Similarity NPD8515 Approved
0.6069 Remote Similarity NPD8517 Approved
0.6069 Remote Similarity NPD8513 Phase 3
0.5985 Remote Similarity NPD7839 Suspended
0.5974 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5956 Remote Similarity NPD8275 Approved
0.5956 Remote Similarity NPD8276 Approved
0.5923 Remote Similarity NPD7983 Approved
0.5909 Remote Similarity NPD8415 Approved
0.5882 Remote Similarity NPD8083 Approved
0.5882 Remote Similarity NPD8139 Approved
0.5882 Remote Similarity NPD8086 Approved
0.5882 Remote Similarity NPD8082 Approved
0.5882 Remote Similarity NPD8138 Approved
0.5882 Remote Similarity NPD8084 Approved
0.5882 Remote Similarity NPD8085 Approved
0.587 Remote Similarity NPD8393 Approved
0.5854 Remote Similarity NPD8389 Clinical (unspecified phase)
0.5797 Remote Similarity NPD8081 Approved
0.5786 Remote Similarity NPD6686 Approved
0.5782 Remote Similarity NPD7299 Clinical (unspecified phase)
0.5755 Remote Similarity NPD4211 Phase 1
0.5752 Remote Similarity NPD5956 Approved
0.5745 Remote Similarity NPD8306 Approved
0.5745 Remote Similarity NPD8305 Approved
0.5745 Remote Similarity NPD6413 Approved
0.5734 Remote Similarity NPD6430 Approved
0.5734 Remote Similarity NPD6429 Approved
0.5725 Remote Similarity NPD46 Approved
0.5725 Remote Similarity NPD6698 Approved
0.5724 Remote Similarity NPD6033 Approved
0.5714 Remote Similarity NPD6412 Phase 2
0.5714 Remote Similarity NPD8307 Discontinued
0.5714 Remote Similarity NPD7260 Phase 2
0.5714 Remote Similarity NPD8140 Approved
0.5704 Remote Similarity NPD6420 Discontinued
0.5664 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5639 Remote Similarity NPD5779 Approved
0.5639 Remote Similarity NPD5778 Approved
0.5638 Remote Similarity NPD8267 Approved
0.5638 Remote Similarity NPD8268 Approved
0.5638 Remote Similarity NPD8266 Approved
0.5638 Remote Similarity NPD8269 Approved
0.5612 Remote Similarity NPD2258 Approved
0.5612 Remote Similarity NPD2259 Approved
0.561 Remote Similarity NPD2575 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