Structure

Physi-Chem Properties

Molecular Weight:  470.25
Volume:  499.763
LogP:  0.978
LogD:  0.3
LogS:  -2.442
# Rotatable Bonds:  13
TPSA:  118.89
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.289
Synthetic Accessibility Score:  4.526
Fsp3:  0.444
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:  -5.039
MDCK Permeability:  1.7966764062293805e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.212
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.016
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  99.7431411743164%
Volume Distribution (VD):  0.155
Pgp-substrate:  0.5971143245697021%

ADMET: Metabolism

CYP1A2-inhibitor:  0.078
CYP1A2-substrate:  0.33
CYP2C19-inhibitor:  0.07
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.895
CYP2C9-substrate:  0.993
CYP2D6-inhibitor:  0.063
CYP2D6-substrate:  0.754
CYP3A4-inhibitor:  0.251
CYP3A4-substrate:  0.177

ADMET: Excretion

Clearance (CL):  1.908
Half-life (T1/2):  0.884

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.928
Drug-inuced Liver Injury (DILI):  0.976
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.186
Maximum Recommended Daily Dose:  0.308
Skin Sensitization:  0.741
Carcinogencity:  0.735
Eye Corrosion:  0.003
Eye Irritation:  0.034
Respiratory Toxicity:  0.286

Download Data

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

  Natural Product: NPC474099

Natural Product ID:  NPC474099
Common Name*:   Sarcotrine E
IUPAC Name:   sodium;2-[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]-5-oxo-2H-pyrrol-1-yl]acetate
Synonyms:   Sarcotrine E
Standard InCHIKey:  HPSAWHHKSTXKBS-UWGYEKCBSA-M
Standard InCHI:  InChI=1S/C27H37NO6.Na/c1-18(10-6-12-20(3)16-23-25(31)21(4)27(33)34-23)8-5-9-19(2)11-7-13-22-14-15-28(26(22)32)17-24(29)30;/h5,8-9,12,14,18,23,31H,6-7,10-11,13,15-17H2,1-4H3,(H,29,30);/q;+1/p-1/b8-5+,19-9+,20-12-;/t18-,23-;/m1./s1
SMILES:  CC1=C(C(OC1=O)CC(=CCCC(C)C=CC=C(C)CCCC2=CCN(C2=O)CC(=O)[O-])C)O.[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL461402
PubChem CID:   54688704
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
NPO33166 Sarcotragus Genus Irciniidae Eukaryota n.a. n.a. n.a. PMID[14640517]

☑ 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 > 30.0 ug ml-1 PMID[517703]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 > 30.0 ug ml-1 PMID[517703]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 > 30.0 ug ml-1 PMID[517703]
NPT574 Cell Line XF498 Homo sapiens ED50 > 30.0 ug ml-1 PMID[517703]
NPT148 Cell Line HCT-15 Homo sapiens ED50 > 30.0 ug ml-1 PMID[517703]

☑ 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 NPC474099 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
0.9596 High Similarity NPC199831
0.9596 High Similarity NPC474827
0.9596 High Similarity NPC474828
0.9596 High Similarity NPC68001
0.9495 High Similarity NPC474244
0.9091 High Similarity NPC52820
0.8868 High Similarity NPC469603
0.8725 High Similarity NPC26597
0.8396 Intermediate Similarity NPC469604
0.7661 Intermediate Similarity NPC213969
0.7661 Intermediate Similarity NPC165726
0.7596 Intermediate Similarity NPC17143
0.7596 Intermediate Similarity NPC47230
0.75 Intermediate Similarity NPC469597
0.7436 Intermediate Similarity NPC472536
0.7436 Intermediate Similarity NPC103391
0.7328 Intermediate Similarity NPC474431
0.7328 Intermediate Similarity NPC474411
0.7264 Intermediate Similarity NPC475995
0.7264 Intermediate Similarity NPC474098
0.7203 Intermediate Similarity NPC193471
0.7203 Intermediate Similarity NPC130124
0.7179 Intermediate Similarity NPC47857
0.7179 Intermediate Similarity NPC181510
0.7179 Intermediate Similarity NPC168758
0.7027 Intermediate Similarity NPC476344
0.7 Intermediate Similarity NPC150041
0.6991 Remote Similarity NPC188785
0.6977 Remote Similarity NPC120335
0.6967 Remote Similarity NPC201889
0.6967 Remote Similarity NPC106791
0.6967 Remote Similarity NPC284656
0.6957 Remote Similarity NPC64168
0.687 Remote Similarity NPC279833
0.687 Remote Similarity NPC80439
0.687 Remote Similarity NPC173690
0.687 Remote Similarity NPC6271
0.6759 Remote Similarity NPC475739
0.675 Remote Similarity NPC316984
0.675 Remote Similarity NPC30911
0.6729 Remote Similarity NPC130436
0.6729 Remote Similarity NPC469861
0.6729 Remote Similarity NPC469860
0.6726 Remote Similarity NPC150967
0.6697 Remote Similarity NPC81195
0.6696 Remote Similarity NPC77703
0.6695 Remote Similarity NPC271562
0.6694 Remote Similarity NPC314550
0.6667 Remote Similarity NPC23963
0.6667 Remote Similarity NPC205176
0.6639 Remote Similarity NPC476276
0.6637 Remote Similarity NPC175614
0.6636 Remote Similarity NPC474424
0.6613 Remote Similarity NPC475642
0.6612 Remote Similarity NPC58281
0.661 Remote Similarity NPC271269
0.661 Remote Similarity NPC476926
0.661 Remote Similarity NPC154601
0.6609 Remote Similarity NPC474985
0.6587 Remote Similarity NPC11379
0.6579 Remote Similarity NPC241426
0.6571 Remote Similarity NPC226982
0.6571 Remote Similarity NPC277341
0.6571 Remote Similarity NPC477217
0.6571 Remote Similarity NPC201244
0.656 Remote Similarity NPC235625
0.6542 Remote Similarity NPC475975
0.6535 Remote Similarity NPC107654
0.6529 Remote Similarity NPC195435
0.6529 Remote Similarity NPC196073
0.6514 Remote Similarity NPC45409
0.65 Remote Similarity NPC476918
0.65 Remote Similarity NPC470072
0.6486 Remote Similarity NPC159568
0.6479 Remote Similarity NPC135121
0.6475 Remote Similarity NPC21713
0.6475 Remote Similarity NPC475608
0.6471 Remote Similarity NPC476328
0.6457 Remote Similarity NPC477143
0.6457 Remote Similarity NPC477140
0.6449 Remote Similarity NPC253801
0.6429 Remote Similarity NPC472264
0.6429 Remote Similarity NPC156336
0.6429 Remote Similarity NPC120599
0.6429 Remote Similarity NPC200412
0.6423 Remote Similarity NPC275100
0.6423 Remote Similarity NPC474497
0.6422 Remote Similarity NPC279267
0.6422 Remote Similarity NPC69082
0.6418 Remote Similarity NPC133089
0.6417 Remote Similarity NPC251330
0.6406 Remote Similarity NPC156379
0.6406 Remote Similarity NPC475383
0.6404 Remote Similarity NPC469739
0.6389 Remote Similarity NPC161670
0.6389 Remote Similarity NPC475706
0.6385 Remote Similarity NPC469999
0.6385 Remote Similarity NPC321197
0.6381 Remote Similarity NPC99651
0.6378 Remote Similarity NPC241050
0.6373 Remote Similarity NPC315843
0.6356 Remote Similarity NPC473289
0.6355 Remote Similarity NPC180363
0.6355 Remote Similarity NPC131002
0.6355 Remote Similarity NPC145914
0.6355 Remote Similarity NPC475159
0.6355 Remote Similarity NPC473780
0.6355 Remote Similarity NPC11332
0.6355 Remote Similarity NPC329829
0.6355 Remote Similarity NPC73310
0.6355 Remote Similarity NPC65930
0.6355 Remote Similarity NPC473712
0.6355 Remote Similarity NPC474028
0.6355 Remote Similarity NPC94875
0.6355 Remote Similarity NPC473529
0.6355 Remote Similarity NPC474439
0.6339 Remote Similarity NPC475879
0.6339 Remote Similarity NPC53240
0.6336 Remote Similarity NPC309525
0.6331 Remote Similarity NPC315210
0.6331 Remote Similarity NPC315848
0.633 Remote Similarity NPC223871
0.633 Remote Similarity NPC322529
0.633 Remote Similarity NPC66346
0.633 Remote Similarity NPC286338
0.633 Remote Similarity NPC473478
0.633 Remote Similarity NPC103284
0.633 Remote Similarity NPC107986
0.633 Remote Similarity NPC231009
0.633 Remote Similarity NPC473669
0.633 Remote Similarity NPC82795
0.633 Remote Similarity NPC110710
0.633 Remote Similarity NPC283085
0.633 Remote Similarity NPC473651
0.633 Remote Similarity NPC132496
0.633 Remote Similarity NPC1083
0.6328 Remote Similarity NPC230849
0.6327 Remote Similarity NPC475342
0.6324 Remote Similarity NPC99864
0.6316 Remote Similarity NPC313265
0.6296 Remote Similarity NPC475714
0.6296 Remote Similarity NPC16488
0.6296 Remote Similarity NPC144415
0.6293 Remote Similarity NPC265662
0.6288 Remote Similarity NPC473249
0.6286 Remote Similarity NPC93763
0.6286 Remote Similarity NPC108816
0.6275 Remote Similarity NPC474705
0.6273 Remote Similarity NPC473687
0.6273 Remote Similarity NPC231096
0.6273 Remote Similarity NPC114694
0.6273 Remote Similarity NPC134807
0.6273 Remote Similarity NPC309211
0.6273 Remote Similarity NPC469483
0.6273 Remote Similarity NPC134885
0.6273 Remote Similarity NPC316426
0.6273 Remote Similarity NPC308412
0.6273 Remote Similarity NPC103523
0.6273 Remote Similarity NPC112685
0.6273 Remote Similarity NPC240695
0.6273 Remote Similarity NPC232555
0.6273 Remote Similarity NPC204686
0.6273 Remote Similarity NPC475581
0.6273 Remote Similarity NPC210218
0.6273 Remote Similarity NPC107717
0.6273 Remote Similarity NPC62118
0.6273 Remote Similarity NPC219498
0.6273 Remote Similarity NPC315395
0.6273 Remote Similarity NPC171174
0.6273 Remote Similarity NPC134865
0.6273 Remote Similarity NPC142117
0.6262 Remote Similarity NPC325031
0.6261 Remote Similarity NPC205546
0.6261 Remote Similarity NPC189764
0.6261 Remote Similarity NPC50902
0.6261 Remote Similarity NPC233273
0.626 Remote Similarity NPC36254
0.625 Remote Similarity NPC476921
0.625 Remote Similarity NPC120420
0.625 Remote Similarity NPC123360
0.6239 Remote Similarity NPC163093
0.6239 Remote Similarity NPC156804
0.6231 Remote Similarity NPC273185
0.6226 Remote Similarity NPC471768
0.622 Remote Similarity NPC476190
0.6216 Remote Similarity NPC160138
0.6216 Remote Similarity NPC178215
0.6216 Remote Similarity NPC324506
0.6195 Remote Similarity NPC476019
0.6195 Remote Similarity NPC473448
0.619 Remote Similarity NPC68156
0.619 Remote Similarity NPC474984
0.6182 Remote Similarity NPC235809
0.6182 Remote Similarity NPC77871
0.6182 Remote Similarity NPC202055
0.6182 Remote Similarity NPC329838
0.6182 Remote Similarity NPC475268
0.6182 Remote Similarity NPC329615
0.6182 Remote Similarity NPC21469
0.6182 Remote Similarity NPC39279

  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 NPC474099 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
0.675 Remote Similarity NPD2204 Approved
0.672 Remote Similarity NPD7299 Clinical (unspecified phase)
0.6639 Remote Similarity NPD1376 Discontinued
0.6484 Remote Similarity NPD7624 Clinical (unspecified phase)
0.6484 Remote Similarity NPD7623 Phase 3
0.6462 Remote Similarity NPD8273 Phase 1
0.6406 Remote Similarity NPD7739 Clinical (unspecified phase)
0.6324 Remote Similarity NPD8415 Approved
0.6311 Remote Similarity NPD1452 Discontinued
0.6299 Remote Similarity NPD7641 Discontinued
0.6288 Remote Similarity NPD7746 Phase 1
0.6288 Remote Similarity NPD7747 Phase 1
0.625 Remote Similarity NPD2495 Phase 3
0.6159 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6103 Remote Similarity NPD7260 Phase 2
0.608 Remote Similarity NPD7116 Clinical (unspecified phase)
0.6066 Remote Similarity NPD777 Phase 3
0.6061 Remote Similarity NPD7642 Approved
0.597 Remote Similarity NPD8451 Approved
0.5969 Remote Similarity NPD7505 Discontinued
0.5942 Remote Similarity NPD6845 Suspended
0.5935 Remote Similarity NPD7333 Discontinued
0.5926 Remote Similarity NPD8448 Approved
0.5923 Remote Similarity NPD1773 Discontinued
0.5913 Remote Similarity NPD7838 Discovery
0.5913 Remote Similarity NPD46 Approved
0.5913 Remote Similarity NPD6698 Approved
0.5878 Remote Similarity NPD3159 Discontinued
0.5833 Remote Similarity NPD8384 Approved
0.5821 Remote Similarity NPD7829 Approved
0.5821 Remote Similarity NPD7830 Approved
0.5814 Remote Similarity NPD1000 Clinical (unspecified phase)
0.5797 Remote Similarity NPD8392 Approved
0.5797 Remote Similarity NPD8391 Approved
0.5797 Remote Similarity NPD8390 Approved
0.5778 Remote Similarity NPD8341 Approved
0.5778 Remote Similarity NPD8299 Approved
0.5778 Remote Similarity NPD8340 Approved
0.5778 Remote Similarity NPD8342 Approved
0.5755 Remote Similarity NPD3662 Phase 3
0.5755 Remote Similarity NPD3661 Approved
0.5755 Remote Similarity NPD3663 Approved
0.5755 Remote Similarity NPD3664 Approved
0.5748 Remote Similarity NPD6421 Discontinued
0.5726 Remote Similarity NPD7983 Approved
0.5725 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5725 Remote Similarity NPD7500 Approved
0.5714 Remote Similarity NPD7154 Phase 3
0.5714 Remote Similarity NPD2645 Approved
0.5703 Remote Similarity NPD7601 Clinical (unspecified phase)
0.568 Remote Similarity NPD4211 Phase 1
0.5678 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5667 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5641 Remote Similarity NPD5785 Approved
0.5635 Remote Similarity NPD7899 Clinical (unspecified phase)
0.563 Remote Similarity NPD8080 Discontinued
0.5625 Remote Similarity NPD6420 Discontinued
0.5625 Remote Similarity NPD5209 Approved
0.562 Remote Similarity NPD2148 Clinical (unspecified phase)
0.562 Remote Similarity NPD2584 Suspended
0.562 Remote Similarity NPD3677 Clinical (unspecified phase)
0.5606 Remote Similarity NPD961 Discontinued

  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