Structure

Physi-Chem Properties

Molecular Weight:  483.33
Volume:  538.026
LogP:  5.381
LogD:  4.878
LogS:  -4.614
# 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:  4.282
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:  -4.857
MDCK Permeability:  2.126667823176831e-05
Pgp-inhibitor:  0.058
Pgp-substrate:  0.025
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.928
30% Bioavailability (F30%):  0.638

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.091
Plasma Protein Binding (PPB):  99.89594268798828%
Volume Distribution (VD):  1.547
Pgp-substrate:  0.742777407169342%

ADMET: Metabolism

CYP1A2-inhibitor:  0.19
CYP1A2-substrate:  0.732
CYP2C19-inhibitor:  0.771
CYP2C19-substrate:  0.488
CYP2C9-inhibitor:  0.66
CYP2C9-substrate:  0.995
CYP2D6-inhibitor:  0.859
CYP2D6-substrate:  0.914
CYP3A4-inhibitor:  0.564
CYP3A4-substrate:  0.235

ADMET: Excretion

Clearance (CL):  6.005
Half-life (T1/2):  0.717

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.767
Drug-inuced Liver Injury (DILI):  0.953
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.308
Maximum Recommended Daily Dose:  0.759
Skin Sensitization:  0.765
Carcinogencity:  0.582
Eye Corrosion:  0.003
Eye Irritation:  0.035
Respiratory Toxicity:  0.532

Download Data

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

  Natural Product: NPC52820

Natural Product ID:  NPC52820
Common Name*:   Sarcotrine D
IUPAC Name:   3-[(4E,6E,8S,11Z)-13-[(2S)-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:   Sarcotrine D
Standard InCHIKey:  MKKHCPKVPZKMNT-QAVDTZCXSA-N
Standard InCHI:  InChI=1S/C30H45NO4/c1-21(2)16-17-31-20-26(19-28(31)32)15-9-13-23(4)11-7-10-22(3)12-8-14-24(5)18-27-29(33)25(6)30(34)35-27/h7,10-11,14,19,21-22,27,33H,8-9,12-13,15-18,20H2,1-6H3/b10-7+,23-11+,24-14-/t22-,27+/m1/s1
SMILES:  CC(C)CCN1CC(=CC1=O)CCC/C(=C/C=C/[C@@H](C)CC/C=C(/C)C[C@H]1C(=C(C)C(=O)O1)O)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL483228
PubChem CID:   54687140
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 = 30.0 ug ml-1 PMID[570136]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 = 25.9 ug ml-1 PMID[570136]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 = 13.2 ug ml-1 PMID[570136]
NPT574 Cell Line XF498 Homo sapiens ED50 = 30.0 ug ml-1 PMID[570136]
NPT148 Cell Line HCT-15 Homo sapiens ED50 = 21.6 ug ml-1 PMID[570136]

☑ 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 NPC52820 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
0.9574 High Similarity NPC474244
0.9474 High Similarity NPC474827
0.9474 High Similarity NPC199831
0.9474 High Similarity NPC474828
0.9474 High Similarity NPC68001
0.9091 High Similarity NPC474099
0.8416 Intermediate Similarity NPC469604
0.82 Intermediate Similarity NPC26597
0.8019 Intermediate Similarity NPC469603
0.75 Intermediate Similarity NPC213969
0.75 Intermediate Similarity NPC165726
0.7129 Intermediate Similarity NPC81195
0.7064 Intermediate Similarity NPC64168
0.7059 Intermediate Similarity NPC475995
0.7059 Intermediate Similarity NPC474098
0.6989 Remote Similarity NPC107654
0.6972 Remote Similarity NPC173690
0.6972 Remote Similarity NPC80439
0.6972 Remote Similarity NPC6271
0.6972 Remote Similarity NPC279833
0.697 Remote Similarity NPC475706
0.6957 Remote Similarity NPC472536
0.6957 Remote Similarity NPC103391
0.6939 Remote Similarity NPC474028
0.6939 Remote Similarity NPC474439
0.687 Remote Similarity NPC193471
0.687 Remote Similarity NPC130124
0.6869 Remote Similarity NPC475714
0.6842 Remote Similarity NPC168758
0.6842 Remote Similarity NPC47857
0.6842 Remote Similarity NPC181510
0.6837 Remote Similarity NPC277341
0.6837 Remote Similarity NPC226982
0.6822 Remote Similarity NPC476344
0.6809 Remote Similarity NPC315843
0.68 Remote Similarity NPC161670
0.6792 Remote Similarity NPC150041
0.6765 Remote Similarity NPC45409
0.6757 Remote Similarity NPC205176
0.6733 Remote Similarity NPC474424
0.6731 Remote Similarity NPC47230
0.6731 Remote Similarity NPC17143
0.6729 Remote Similarity NPC175614
0.6726 Remote Similarity NPC470072
0.6724 Remote Similarity NPC469597
0.6697 Remote Similarity NPC474985
0.6696 Remote Similarity NPC30911
0.6696 Remote Similarity NPC316984
0.6667 Remote Similarity NPC469860
0.6667 Remote Similarity NPC469861
0.6667 Remote Similarity NPC473361
0.6667 Remote Similarity NPC130436
0.6667 Remote Similarity NPC150967
0.6667 Remote Similarity NPC472264
0.6667 Remote Similarity NPC329904
0.6639 Remote Similarity NPC106791
0.6639 Remote Similarity NPC284656
0.6639 Remote Similarity NPC201889
0.6636 Remote Similarity NPC77703
0.6636 Remote Similarity NPC189764
0.6636 Remote Similarity NPC233273
0.6636 Remote Similarity NPC205546
0.6636 Remote Similarity NPC50902
0.6636 Remote Similarity NPC188785
0.6634 Remote Similarity NPC475975
0.6633 Remote Similarity NPC99651
0.6633 Remote Similarity NPC471768
0.6632 Remote Similarity NPC470686
0.6596 Remote Similarity NPC316185
0.6577 Remote Similarity NPC473289
0.6571 Remote Similarity NPC159568
0.6552 Remote Similarity NPC474411
0.6552 Remote Similarity NPC474431
0.6538 Remote Similarity NPC475739
0.6514 Remote Similarity NPC241426
0.6486 Remote Similarity NPC175531
0.6466 Remote Similarity NPC122926
0.6466 Remote Similarity NPC196073
0.6466 Remote Similarity NPC195435
0.6466 Remote Similarity NPC113012
0.6452 Remote Similarity NPC474823
0.6449 Remote Similarity NPC29798
0.6449 Remote Similarity NPC282644
0.6417 Remote Similarity NPC475642
0.6415 Remote Similarity NPC475879
0.6415 Remote Similarity NPC53240
0.641 Remote Similarity NPC58281
0.6406 Remote Similarity NPC120335
0.6404 Remote Similarity NPC154601
0.6404 Remote Similarity NPC271269
0.6393 Remote Similarity NPC477143
0.6393 Remote Similarity NPC477140
0.6387 Remote Similarity NPC474984
0.6383 Remote Similarity NPC475004
0.6356 Remote Similarity NPC275100
0.6356 Remote Similarity NPC314550
0.6356 Remote Similarity NPC279383
0.6356 Remote Similarity NPC474497
0.6341 Remote Similarity NPC23963
0.6328 Remote Similarity NPC477988
0.6316 Remote Similarity NPC59558
0.6303 Remote Similarity NPC475988
0.63 Remote Similarity NPC471537
0.6293 Remote Similarity NPC476276
0.6281 Remote Similarity NPC65045
0.6275 Remote Similarity NPC16321
0.6271 Remote Similarity NPC475608
0.6271 Remote Similarity NPC21713
0.627 Remote Similarity NPC329401
0.627 Remote Similarity NPC477987
0.626 Remote Similarity NPC11379
0.625 Remote Similarity NPC316730
0.6238 Remote Similarity NPC209232
0.6237 Remote Similarity NPC191233
0.623 Remote Similarity NPC120599
0.623 Remote Similarity NPC200412
0.623 Remote Similarity NPC235625
0.623 Remote Similarity NPC156336
0.6224 Remote Similarity NPC478193
0.6224 Remote Similarity NPC478192
0.6224 Remote Similarity NPC34672
0.6224 Remote Similarity NPC478195
0.6224 Remote Similarity NPC478194
0.6224 Remote Similarity NPC478191
0.6224 Remote Similarity NPC478196
0.6218 Remote Similarity NPC474995
0.6218 Remote Similarity NPC295444
0.6218 Remote Similarity NPC273215
0.6218 Remote Similarity NPC268327
0.6214 Remote Similarity NPC16488
0.6214 Remote Similarity NPC253801
0.6214 Remote Similarity NPC161045
0.6211 Remote Similarity NPC90782
0.6211 Remote Similarity NPC470693
0.6211 Remote Similarity NPC151481
0.621 Remote Similarity NPC475383
0.621 Remote Similarity NPC156379
0.6207 Remote Similarity NPC251330
0.6204 Remote Similarity NPC72183
0.6204 Remote Similarity NPC118844
0.6204 Remote Similarity NPC299808
0.6204 Remote Similarity NPC110875
0.62 Remote Similarity NPC279532
0.6195 Remote Similarity NPC474873
0.619 Remote Similarity NPC279267
0.619 Remote Similarity NPC69082
0.6186 Remote Similarity NPC326126
0.6179 Remote Similarity NPC241050
0.6176 Remote Similarity NPC474894
0.6154 Remote Similarity NPC471636
0.6154 Remote Similarity NPC287572
0.6148 Remote Similarity NPC315210
0.6148 Remote Similarity NPC315848
0.6139 Remote Similarity NPC271632
0.6129 Remote Similarity NPC220766
0.6129 Remote Similarity NPC182794
0.6129 Remote Similarity NPC282760
0.6121 Remote Similarity NPC476328
0.6117 Remote Similarity NPC131002
0.6117 Remote Similarity NPC65930
0.6117 Remote Similarity NPC94875
0.6117 Remote Similarity NPC475159
0.6117 Remote Similarity NPC473529
0.6117 Remote Similarity NPC11332
0.6117 Remote Similarity NPC473780
0.6117 Remote Similarity NPC180363
0.6117 Remote Similarity NPC145914
0.6117 Remote Similarity NPC329829
0.6117 Remote Similarity NPC473712
0.6117 Remote Similarity NPC73310
0.6106 Remote Similarity NPC233932
0.6105 Remote Similarity NPC310210
0.6102 Remote Similarity NPC474891
0.6102 Remote Similarity NPC24389
0.61 Remote Similarity NPC315394
0.61 Remote Similarity NPC68156
0.6095 Remote Similarity NPC471494
0.6095 Remote Similarity NPC132496
0.6095 Remote Similarity NPC11804
0.6095 Remote Similarity NPC103284
0.6095 Remote Similarity NPC322529
0.6095 Remote Similarity NPC110710
0.6095 Remote Similarity NPC286338
0.6095 Remote Similarity NPC1083
0.6095 Remote Similarity NPC223871
0.6095 Remote Similarity NPC283085
0.6095 Remote Similarity NPC473669
0.6095 Remote Similarity NPC473478
0.6095 Remote Similarity NPC231009
0.6095 Remote Similarity NPC82795
0.6095 Remote Similarity NPC107986
0.6095 Remote Similarity NPC66346
0.6095 Remote Similarity NPC473651
0.6087 Remote Similarity NPC210303
0.6087 Remote Similarity NPC179087
0.6087 Remote Similarity NPC44343
0.6083 Remote Similarity NPC43648
0.608 Remote Similarity NPC470000
0.6075 Remote Similarity NPC260343
0.6071 Remote Similarity NPC265662

  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 NPC52820 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
0.6696 Remote Similarity NPD2204 Approved
0.64 Remote Similarity NPD8273 Phase 1
0.6281 Remote Similarity NPD7505 Discontinued
0.6262 Remote Similarity NPD7838 Discovery
0.626 Remote Similarity NPD7299 Clinical (unspecified phase)
0.6061 Remote Similarity NPD1452 Discontinued
0.6048 Remote Similarity NPD2495 Phase 3
0.6033 Remote Similarity NPD1376 Discontinued
0.6032 Remote Similarity NPD7624 Clinical (unspecified phase)
0.6032 Remote Similarity NPD7623 Phase 3
0.5983 Remote Similarity NPD4211 Phase 1
0.5952 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5909 Remote Similarity NPD7260 Phase 2
0.5847 Remote Similarity NPD777 Phase 3
0.5847 Remote Similarity NPD7333 Discontinued
0.5846 Remote Similarity NPD7746 Phase 1
0.5846 Remote Similarity NPD7747 Phase 1
0.584 Remote Similarity NPD7641 Discontinued
0.5818 Remote Similarity NPD6698 Approved
0.5818 Remote Similarity NPD46 Approved
0.5778 Remote Similarity NPD8415 Approved
0.5746 Remote Similarity NPD6845 Suspended
0.5739 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5738 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5701 Remote Similarity NPD6400 Clinical (unspecified phase)
0.566 Remote Similarity NPD5209 Approved
0.5649 Remote Similarity NPD8451 Approved
0.5638 Remote Similarity NPD3205 Discontinued
0.5625 Remote Similarity NPD7983 Approved
0.562 Remote Similarity NPD8387 Clinical (unspecified phase)
0.562 Remote Similarity NPD8065 Phase 2
0.5615 Remote Similarity NPD7642 Approved
0.561 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5607 Remote Similarity NPD205 Approved
0.5607 Remote Similarity NPD7154 Phase 3
0.5606 Remote Similarity NPD8448 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