Structure

Physi-Chem Properties

Molecular Weight:  483.33
Volume:  538.026
LogP:  5.243
LogD:  4.942
LogS:  -4.911
# Rotatable Bonds:  14
TPSA:  78.76
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.188
Synthetic Accessibility Score:  4.233
Fsp3:  0.533
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.826
MDCK Permeability:  2.3819708076189272e-05
Pgp-inhibitor:  0.075
Pgp-substrate:  0.026
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.597
30% Bioavailability (F30%):  0.318

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.04
Plasma Protein Binding (PPB):  100.14833068847656%
Volume Distribution (VD):  1.474
Pgp-substrate:  0.8827568292617798%

ADMET: Metabolism

CYP1A2-inhibitor:  0.186
CYP1A2-substrate:  0.756
CYP2C19-inhibitor:  0.484
CYP2C19-substrate:  0.409
CYP2C9-inhibitor:  0.652
CYP2C9-substrate:  0.993
CYP2D6-inhibitor:  0.765
CYP2D6-substrate:  0.913
CYP3A4-inhibitor:  0.448
CYP3A4-substrate:  0.234

ADMET: Excretion

Clearance (CL):  5.688
Half-life (T1/2):  0.659

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.837
Drug-inuced Liver Injury (DILI):  0.963
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.289
Maximum Recommended Daily Dose:  0.353
Skin Sensitization:  0.734
Carcinogencity:  0.628
Eye Corrosion:  0.003
Eye Irritation:  0.067
Respiratory Toxicity:  0.457

Download Data

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

  Natural Product: NPC68001

Natural Product ID:  NPC68001
Common Name*:   Epi-Sarcotrine A
IUPAC Name:   4-[(4E,6E,8S,11Z)-13-[(2R)-3-hydroxy-4-methyl-5-oxo-2H-furan-2-yl]-4,8,12-trimethyltrideca-4,6,11-trienyl]-1-(3-methylbutyl)-2H-pyrrol-5-one
Synonyms:  
Standard InCHIKey:  IDSXOIOXEMBIDK-YBQSNTSBSA-N
Standard InCHI:  InChI=1S/C30H45NO4/c1-21(2)16-18-31-19-17-26(29(31)33)15-9-13-23(4)11-7-10-22(3)12-8-14-24(5)20-27-28(32)25(6)30(34)35-27/h7,10-11,14,17,21-22,27,32H,8-9,12-13,15-16,18-20H2,1-6H3/b10-7+,23-11+,24-14-/t22-,27-/m1/s1
SMILES:  CC(C)CCN1CC=C(CCC/C(=C/C=C/[C@@H](C)CC/C=C(/C)C[C@@H]2C(=C(C)C(=O)O2)O)/C)C1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL489753
PubChem CID:   54703274
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001538] Diterpene lactones

*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
NPO33064 sarcotragus sp. Species Irciniidae Eukaryota n.a. n.a. n.a. PMID[11678655]
NPO33064 sarcotragus sp. Species Irciniidae Eukaryota n.a. n.a. n.a. PMID[12350153]
NPO33064 sarcotragus sp. Species Irciniidae Eukaryota n.a. n.a. n.a. PMID[18341287]

☑ 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
NPT81 Cell Line A549 Homo sapiens ED50 = 4.3 ug ml-1 PMID[508330]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 = 4.0 ug ml-1 PMID[508330]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 = 3.4 ug ml-1 PMID[508330]
NPT574 Cell Line XF498 Homo sapiens ED50 = 3.9 ug ml-1 PMID[508330]
NPT148 Cell Line HCT-15 Homo sapiens ED50 = 3.8 ug ml-1 PMID[508330]

☑ 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 NPC68001 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 NPC474827
1.0 High Similarity NPC474828
1.0 High Similarity NPC199831
0.9596 High Similarity NPC474099
0.9474 High Similarity NPC52820
0.9091 High Similarity NPC474244
0.8491 Intermediate Similarity NPC469603
0.8333 Intermediate Similarity NPC26597
0.8019 Intermediate Similarity NPC469604
0.7917 Intermediate Similarity NPC165726
0.7917 Intermediate Similarity NPC213969
0.7549 Intermediate Similarity NPC474098
0.7549 Intermediate Similarity NPC475995
0.729 Intermediate Similarity NPC476344
0.7264 Intermediate Similarity NPC150041
0.7212 Intermediate Similarity NPC47230
0.7212 Intermediate Similarity NPC17143
0.7155 Intermediate Similarity NPC193471
0.7155 Intermediate Similarity NPC130124
0.7155 Intermediate Similarity NPC469597
0.713 Intermediate Similarity NPC47857
0.713 Intermediate Similarity NPC168758
0.713 Intermediate Similarity NPC181510
0.7094 Intermediate Similarity NPC103391
0.7094 Intermediate Similarity NPC472536
0.7019 Intermediate Similarity NPC475739
0.699 Remote Similarity NPC469861
0.699 Remote Similarity NPC130436
0.699 Remote Similarity NPC469860
0.6983 Remote Similarity NPC474431
0.6983 Remote Similarity NPC474411
0.6972 Remote Similarity NPC150967
0.6952 Remote Similarity NPC81195
0.6937 Remote Similarity NPC77703
0.6917 Remote Similarity NPC201889
0.6917 Remote Similarity NPC106791
0.6917 Remote Similarity NPC284656
0.6903 Remote Similarity NPC64168
0.6893 Remote Similarity NPC474424
0.6842 Remote Similarity NPC271269
0.6842 Remote Similarity NPC154601
0.6838 Remote Similarity NPC58281
0.6833 Remote Similarity NPC475642
0.6832 Remote Similarity NPC277341
0.6832 Remote Similarity NPC226982
0.6818 Remote Similarity NPC241426
0.6814 Remote Similarity NPC6271
0.6814 Remote Similarity NPC80439
0.6814 Remote Similarity NPC173690
0.6814 Remote Similarity NPC279833
0.6804 Remote Similarity NPC107654
0.6762 Remote Similarity NPC45409
0.6752 Remote Similarity NPC195435
0.6752 Remote Similarity NPC196073
0.6729 Remote Similarity NPC159568
0.6727 Remote Similarity NPC175614
0.6724 Remote Similarity NPC470072
0.6699 Remote Similarity NPC253801
0.6695 Remote Similarity NPC30911
0.6695 Remote Similarity NPC475608
0.6695 Remote Similarity NPC21713
0.6695 Remote Similarity NPC316984
0.6667 Remote Similarity NPC279267
0.6667 Remote Similarity NPC477143
0.6667 Remote Similarity NPC477140
0.6667 Remote Similarity NPC472264
0.6667 Remote Similarity NPC120335
0.6667 Remote Similarity NPC69082
0.6639 Remote Similarity NPC275100
0.6639 Remote Similarity NPC120599
0.6639 Remote Similarity NPC474497
0.6639 Remote Similarity NPC314550
0.6639 Remote Similarity NPC156336
0.6639 Remote Similarity NPC200412
0.6638 Remote Similarity NPC251330
0.6637 Remote Similarity NPC188785
0.6635 Remote Similarity NPC161670
0.6635 Remote Similarity NPC475706
0.6634 Remote Similarity NPC99651
0.6633 Remote Similarity NPC315843
0.6613 Remote Similarity NPC23963
0.6613 Remote Similarity NPC475383
0.6613 Remote Similarity NPC156379
0.6602 Remote Similarity NPC73310
0.6602 Remote Similarity NPC475159
0.6602 Remote Similarity NPC329829
0.6602 Remote Similarity NPC145914
0.6602 Remote Similarity NPC473780
0.6602 Remote Similarity NPC65930
0.6602 Remote Similarity NPC473712
0.6602 Remote Similarity NPC11332
0.6602 Remote Similarity NPC474028
0.6602 Remote Similarity NPC94875
0.6602 Remote Similarity NPC180363
0.6602 Remote Similarity NPC131002
0.6602 Remote Similarity NPC473529
0.6602 Remote Similarity NPC474439
0.6585 Remote Similarity NPC241050
0.6581 Remote Similarity NPC476276
0.6574 Remote Similarity NPC475879
0.6571 Remote Similarity NPC283085
0.6571 Remote Similarity NPC107986
0.6571 Remote Similarity NPC1083
0.6571 Remote Similarity NPC132496
0.6571 Remote Similarity NPC223871
0.6571 Remote Similarity NPC473651
0.6571 Remote Similarity NPC231009
0.6571 Remote Similarity NPC286338
0.6571 Remote Similarity NPC103284
0.6571 Remote Similarity NPC82795
0.6571 Remote Similarity NPC110710
0.6571 Remote Similarity NPC66346
0.6571 Remote Similarity NPC473478
0.6571 Remote Similarity NPC322529
0.6571 Remote Similarity NPC473669
0.6549 Remote Similarity NPC474985
0.6538 Remote Similarity NPC16488
0.6538 Remote Similarity NPC475714
0.6538 Remote Similarity NPC144415
0.6535 Remote Similarity NPC93763
0.6535 Remote Similarity NPC108816
0.6532 Remote Similarity NPC11379
0.6531 Remote Similarity NPC474705
0.6518 Remote Similarity NPC265662
0.6509 Remote Similarity NPC473687
0.6509 Remote Similarity NPC315395
0.6509 Remote Similarity NPC210218
0.6509 Remote Similarity NPC107717
0.6509 Remote Similarity NPC316426
0.6509 Remote Similarity NPC134807
0.6509 Remote Similarity NPC308412
0.6509 Remote Similarity NPC309211
0.6509 Remote Similarity NPC142117
0.6509 Remote Similarity NPC219498
0.6509 Remote Similarity NPC475581
0.6509 Remote Similarity NPC231096
0.6509 Remote Similarity NPC134865
0.6509 Remote Similarity NPC103523
0.6509 Remote Similarity NPC114694
0.6509 Remote Similarity NPC232555
0.6509 Remote Similarity NPC62118
0.6509 Remote Similarity NPC240695
0.6509 Remote Similarity NPC204686
0.6509 Remote Similarity NPC171174
0.6509 Remote Similarity NPC469483
0.6509 Remote Similarity NPC112685
0.6509 Remote Similarity NPC134885
0.6505 Remote Similarity NPC325031
0.6504 Remote Similarity NPC235625
0.65 Remote Similarity NPC123360
0.6486 Remote Similarity NPC50902
0.6486 Remote Similarity NPC189764
0.6486 Remote Similarity NPC233273
0.6486 Remote Similarity NPC205546
0.6476 Remote Similarity NPC475975
0.6476 Remote Similarity NPC163093
0.6476 Remote Similarity NPC156804
0.6471 Remote Similarity NPC471768
0.6466 Remote Similarity NPC205176
0.6449 Remote Similarity NPC178215
0.6449 Remote Similarity NPC160138
0.6436 Remote Similarity NPC68156
0.6429 Remote Similarity NPC84038
0.6429 Remote Similarity NPC316185
0.6422 Remote Similarity NPC473448
0.6415 Remote Similarity NPC77871
0.6415 Remote Similarity NPC120398
0.6415 Remote Similarity NPC202055
0.6415 Remote Similarity NPC475268
0.6415 Remote Similarity NPC471567
0.6415 Remote Similarity NPC477013
0.6415 Remote Similarity NPC21469
0.6415 Remote Similarity NPC319036
0.6415 Remote Similarity NPC329838
0.6415 Remote Similarity NPC9678
0.6415 Remote Similarity NPC25764
0.6415 Remote Similarity NPC477018
0.6415 Remote Similarity NPC39167
0.6415 Remote Similarity NPC473156
0.6415 Remote Similarity NPC182383
0.6415 Remote Similarity NPC470400
0.6415 Remote Similarity NPC329615
0.6415 Remote Similarity NPC473671
0.6415 Remote Similarity NPC100921
0.6415 Remote Similarity NPC477014
0.6415 Remote Similarity NPC292809
0.6415 Remote Similarity NPC39279
0.6415 Remote Similarity NPC235809
0.641 Remote Similarity NPC476328
0.64 Remote Similarity NPC478192
0.64 Remote Similarity NPC478196
0.64 Remote Similarity NPC478191
0.64 Remote Similarity NPC478195
0.64 Remote Similarity NPC478193
0.64 Remote Similarity NPC478194
0.6389 Remote Similarity NPC233551
0.6389 Remote Similarity NPC81045
0.6389 Remote Similarity NPC320569
0.6389 Remote Similarity NPC280621
0.6389 Remote Similarity NPC133730

  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 NPC68001 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
0.6695 Remote Similarity NPD2204 Approved
0.6667 Remote Similarity NPD7299 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8273 Phase 1
0.6429 Remote Similarity NPD7623 Phase 3
0.6429 Remote Similarity NPD7624 Clinical (unspecified phase)
0.6349 Remote Similarity NPD7739 Clinical (unspecified phase)
0.6311 Remote Similarity NPD1376 Discontinued
0.6288 Remote Similarity NPD7260 Phase 2
0.624 Remote Similarity NPD7641 Discontinued
0.6238 Remote Similarity NPD1452 Discontinued
0.6231 Remote Similarity NPD7747 Phase 1
0.6231 Remote Similarity NPD7746 Phase 1
0.6148 Remote Similarity NPD7116 Clinical (unspecified phase)
0.6134 Remote Similarity NPD7333 Discontinued
0.6126 Remote Similarity NPD46 Approved
0.6126 Remote Similarity NPD6698 Approved
0.6126 Remote Similarity NPD7838 Discovery
0.6119 Remote Similarity NPD6845 Suspended
0.6032 Remote Similarity NPD7505 Discontinued
0.6029 Remote Similarity NPD8415 Approved
0.6 Remote Similarity NPD7642 Approved
0.5938 Remote Similarity NPD2495 Phase 3
0.5929 Remote Similarity NPD7983 Approved
0.5926 Remote Similarity NPD7154 Phase 3
0.5909 Remote Similarity NPD8451 Approved
0.5878 Remote Similarity NPD7829 Approved
0.5878 Remote Similarity NPD7830 Approved
0.587 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5865 Remote Similarity NPD8448 Approved
0.5862 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5841 Remote Similarity NPD5785 Approved
0.5833 Remote Similarity NPD5209 Approved
0.582 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5806 Remote Similarity NPD6421 Discontinued
0.5806 Remote Similarity NPD6420 Discontinued
0.5781 Remote Similarity NPD7500 Approved
0.578 Remote Similarity NPD5362 Discontinued
0.5763 Remote Similarity NPD8029 Clinical (unspecified phase)
0.576 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5755 Remote Similarity NPD8065 Phase 2
0.5739 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5738 Remote Similarity NPD4211 Phase 1
0.5738 Remote Similarity NPD777 Phase 3
0.5735 Remote Similarity NPD8392 Approved
0.5735 Remote Similarity NPD8390 Approved
0.5735 Remote Similarity NPD8391 Approved
0.5714 Remote Similarity NPD8341 Approved
0.5714 Remote Similarity NPD8299 Approved
0.5714 Remote Similarity NPD8340 Approved
0.5714 Remote Similarity NPD8342 Approved
0.5693 Remote Similarity NPD3664 Approved
0.5693 Remote Similarity NPD3662 Phase 3
0.5693 Remote Similarity NPD3663 Approved
0.5693 Remote Similarity NPD3661 Approved
0.5676 Remote Similarity NPD5363 Approved
0.5662 Remote Similarity NPD2627 Approved
0.5662 Remote Similarity NPD2628 Approved
0.5662 Remote Similarity NPD2160 Approved
0.5662 Remote Similarity NPD2625 Approved
0.5662 Remote Similarity NPD2626 Approved
0.5662 Remote Similarity NPD2159 Approved
0.566 Remote Similarity NPD4756 Discovery
0.5659 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5645 Remote Similarity NPD6686 Approved
0.5641 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5615 Remote Similarity NPD1773 Discontinued
0.5606 Remote Similarity NPD8444 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