Structure

Physi-Chem Properties

Molecular Weight:  222.13
Volume:  240.673
LogP:  4.102
LogD:  3.904
LogS:  -3.319
# Rotatable Bonds:  5
TPSA:  53.6
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.589
Synthetic Accessibility Score:  3.307
Fsp3:  0.385
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.688
MDCK Permeability:  2.54E-05
Pgp-inhibitor:  0
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.196
Plasma Protein Binding (PPB):  99.50%
Volume Distribution (VD):  1.929
Pgp-substrate:  2.44%

ADMET: Metabolism

CYP1A2-inhibitor:  0.304
CYP1A2-substrate:  0.838
CYP2C19-inhibitor:  0.038
CYP2C19-substrate:  0.286
CYP2C9-inhibitor:  0.151
CYP2C9-substrate:  0.888
CYP2D6-inhibitor:  0.066
CYP2D6-substrate:  0.862
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.144

ADMET: Excretion

Clearance (CL):  8.626
Half-life (T1/2):  0.845

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.495
Drug-inuced Liver Injury (DILI):  0.164
AMES Toxicity:  0.18
Rat Oral Acute Toxicity:  0.948
Maximum Recommended Daily Dose:  0.846
Skin Sensitization:  0.952
Carcinogencity:  0.813
Eye Corrosion:  0.59
Eye Irritation:  0.749
Respiratory Toxicity:  0.923

Download Data

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

  Natural Product: NPC478117

Natural Product ID:  NPC478117
Common Name*:   Tricladolide D
IUPAC Name:   3-methyl-4-[(E)-oct-1-enyl]furan-2,5-dione
Synonyms:  
Standard InCHIKey:  CHGNHJANWFHRHG-CMDGGOBGSA-N
Standard InCHI:  InChI=1S/C13H18O3/c1-3-4-5-6-7-8-9-11-10(2)12(14)16-13(11)15/h8-9H,3-7H2,1-2H3/b9-8+
SMILES:  CCCCCC/C=C/C1=C(C(=O)OC1=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11708371
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans
        • [CHEMONTID:0001982] Furanones
          • [CHEMONTID:0002223] Butenolides

*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
NPO33628 Tricladium castaneicola Species Helotiaceae Eukaryota n.a. n.a. n.a. PMID[25875311]
NPO33628 Tricladium castaneicola Species Helotiaceae Eukaryota n.a. Hakone, Kanagawa, Japan n.a. PMID[25875311]

☑ 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
NPT319 Cell Line B16 Mus musculus IC50 = 80000 nM PMID[25875311]

☑ 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 NPC478117 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
0.9057 High Similarity NPC478120
0.8793 High Similarity NPC179087
0.8793 High Similarity NPC44343
0.8793 High Similarity NPC210303
0.85 High Similarity NPC182794
0.85 High Similarity NPC133904
0.8276 Intermediate Similarity NPC133600
0.8276 Intermediate Similarity NPC286189
0.8226 Intermediate Similarity NPC225272
0.8095 Intermediate Similarity NPC474823
0.7969 Intermediate Similarity NPC475004
0.7963 Intermediate Similarity NPC15789
0.7963 Intermediate Similarity NPC236338
0.7885 Intermediate Similarity NPC270706
0.7869 Intermediate Similarity NPC132243
0.7869 Intermediate Similarity NPC473737
0.7797 Intermediate Similarity NPC189700
0.7778 Intermediate Similarity NPC191233
0.7759 Intermediate Similarity NPC245002
0.7736 Intermediate Similarity NPC128280
0.7679 Intermediate Similarity NPC106531
0.7656 Intermediate Similarity NPC21998
0.7619 Intermediate Similarity NPC220766
0.7619 Intermediate Similarity NPC471556
0.7619 Intermediate Similarity NPC131174
0.7619 Intermediate Similarity NPC470688
0.7547 Intermediate Similarity NPC47946
0.7547 Intermediate Similarity NPC26600
0.7541 Intermediate Similarity NPC130953
0.75 Intermediate Similarity NPC248125
0.75 Intermediate Similarity NPC474084
0.7458 Intermediate Similarity NPC221763
0.7455 Intermediate Similarity NPC135698
0.7424 Intermediate Similarity NPC470693
0.7419 Intermediate Similarity NPC151648
0.7414 Intermediate Similarity NPC159535
0.7414 Intermediate Similarity NPC151761
0.7414 Intermediate Similarity NPC269615
0.7407 Intermediate Similarity NPC197467
0.7368 Intermediate Similarity NPC191643
0.7344 Intermediate Similarity NPC471565
0.7344 Intermediate Similarity NPC471566
0.7333 Intermediate Similarity NPC474825
0.7321 Intermediate Similarity NPC27264
0.7302 Intermediate Similarity NPC155849
0.7288 Intermediate Similarity NPC173157
0.7286 Intermediate Similarity NPC4509
0.7273 Intermediate Similarity NPC218477
0.7258 Intermediate Similarity NPC309408
0.7258 Intermediate Similarity NPC98519
0.7231 Intermediate Similarity NPC37382
0.7213 Intermediate Similarity NPC254095
0.7193 Intermediate Similarity NPC148056
0.7188 Intermediate Similarity NPC475618
0.7167 Intermediate Similarity NPC150717
0.7167 Intermediate Similarity NPC86948
0.7164 Intermediate Similarity NPC265574
0.7164 Intermediate Similarity NPC232812
0.7143 Intermediate Similarity NPC234084
0.7143 Intermediate Similarity NPC15912
0.7121 Intermediate Similarity NPC203335
0.7119 Intermediate Similarity NPC218486
0.7101 Intermediate Similarity NPC287878
0.7097 Intermediate Similarity NPC22897
0.7097 Intermediate Similarity NPC159650
0.7097 Intermediate Similarity NPC82465
0.7069 Intermediate Similarity NPC151919
0.7059 Intermediate Similarity NPC37929
0.7059 Intermediate Similarity NPC64234
0.7049 Intermediate Similarity NPC293437
0.7049 Intermediate Similarity NPC249850
0.7049 Intermediate Similarity NPC294938
0.7049 Intermediate Similarity NPC129150
0.7049 Intermediate Similarity NPC135863
0.7037 Intermediate Similarity NPC304079
0.7037 Intermediate Similarity NPC6963
0.7031 Intermediate Similarity NPC68110
0.7015 Intermediate Similarity NPC276290
0.7015 Intermediate Similarity NPC470256
0.7015 Intermediate Similarity NPC313444
0.7 Intermediate Similarity NPC470686
0.6984 Remote Similarity NPC429928
0.6981 Remote Similarity NPC57923
0.697 Remote Similarity NPC315115
0.6935 Remote Similarity NPC223679
0.6935 Remote Similarity NPC21946
0.6923 Remote Similarity NPC173409
0.6923 Remote Similarity NPC226066
0.6923 Remote Similarity NPC53136
0.6901 Remote Similarity NPC329826
0.6901 Remote Similarity NPC469414
0.6897 Remote Similarity NPC43053
0.6885 Remote Similarity NPC96663
0.6875 Remote Similarity NPC217537
0.6866 Remote Similarity NPC472266
0.6866 Remote Similarity NPC194871
0.6857 Remote Similarity NPC474705
0.6825 Remote Similarity NPC222852
0.6818 Remote Similarity NPC476589
0.6818 Remote Similarity NPC282760
0.6812 Remote Similarity NPC59558
0.6812 Remote Similarity NPC67183
0.6812 Remote Similarity NPC315285
0.6812 Remote Similarity NPC316029
0.6812 Remote Similarity NPC315597
0.6786 Remote Similarity NPC308331
0.6769 Remote Similarity NPC217940
0.6769 Remote Similarity NPC474658
0.6765 Remote Similarity NPC477117
0.6765 Remote Similarity NPC287705
0.6727 Remote Similarity NPC12907
0.6724 Remote Similarity NPC275316
0.6724 Remote Similarity NPC221467
0.6721 Remote Similarity NPC474913
0.6719 Remote Similarity NPC26223
0.6719 Remote Similarity NPC299730
0.6719 Remote Similarity NPC79756
0.6716 Remote Similarity NPC116013
0.6716 Remote Similarity NPC146811
0.6714 Remote Similarity NPC257618
0.6714 Remote Similarity NPC316185
0.6714 Remote Similarity NPC186531
0.6714 Remote Similarity NPC84038
0.6712 Remote Similarity NPC54996
0.6712 Remote Similarity NPC473825
0.6711 Remote Similarity NPC16321
0.6711 Remote Similarity NPC268122
0.6711 Remote Similarity NPC94200
0.6667 Remote Similarity NPC478195
0.6667 Remote Similarity NPC187922
0.6667 Remote Similarity NPC151481
0.6667 Remote Similarity NPC90490
0.6667 Remote Similarity NPC478192
0.6667 Remote Similarity NPC478196
0.6667 Remote Similarity NPC478191
0.6667 Remote Similarity NPC478193
0.6667 Remote Similarity NPC34883
0.6667 Remote Similarity NPC268827
0.6667 Remote Similarity NPC478194
0.6623 Remote Similarity NPC118423
0.6622 Remote Similarity NPC184737
0.662 Remote Similarity NPC222244
0.662 Remote Similarity NPC16349
0.662 Remote Similarity NPC276336
0.6618 Remote Similarity NPC132286
0.6615 Remote Similarity NPC329416
0.6615 Remote Similarity NPC317177
0.6615 Remote Similarity NPC15193
0.6615 Remote Similarity NPC317025
0.6615 Remote Similarity NPC326645
0.6604 Remote Similarity NPC123357
0.6579 Remote Similarity NPC42470
0.6575 Remote Similarity NPC123360
0.6571 Remote Similarity NPC476037
0.6571 Remote Similarity NPC476012
0.6571 Remote Similarity NPC469660
0.6567 Remote Similarity NPC273600
0.6567 Remote Similarity NPC470123
0.6562 Remote Similarity NPC478095
0.6557 Remote Similarity NPC474127
0.6552 Remote Similarity NPC82446
0.6533 Remote Similarity NPC264227
0.6533 Remote Similarity NPC63649
0.6533 Remote Similarity NPC472965
0.6528 Remote Similarity NPC315843
0.6528 Remote Similarity NPC15499
0.6528 Remote Similarity NPC474758
0.6528 Remote Similarity NPC117746
0.6528 Remote Similarity NPC107654
0.6528 Remote Similarity NPC259599
0.6528 Remote Similarity NPC476355
0.6528 Remote Similarity NPC294434
0.6522 Remote Similarity NPC238223
0.6515 Remote Similarity NPC475073
0.6515 Remote Similarity NPC2328
0.6515 Remote Similarity NPC474774
0.6508 Remote Similarity NPC44542
0.6508 Remote Similarity NPC471279
0.6508 Remote Similarity NPC471277
0.6508 Remote Similarity NPC265551
0.6508 Remote Similarity NPC212730
0.6494 Remote Similarity NPC324170
0.6491 Remote Similarity NPC100380
0.6486 Remote Similarity NPC68156
0.6486 Remote Similarity NPC471225
0.6479 Remote Similarity NPC293114
0.6479 Remote Similarity NPC181587
0.6479 Remote Similarity NPC163003
0.6471 Remote Similarity NPC9290
0.6471 Remote Similarity NPC475675
0.6471 Remote Similarity NPC276299
0.6471 Remote Similarity NPC475555
0.6462 Remote Similarity NPC19241
0.6452 Remote Similarity NPC25038
0.6438 Remote Similarity NPC68624
0.6438 Remote Similarity NPC260396
0.6438 Remote Similarity NPC329852
0.6429 Remote Similarity NPC476059
0.6429 Remote Similarity NPC236208
0.6429 Remote Similarity NPC473603

  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 NPC478117 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
0.7455 Intermediate Similarity NPD4220 Pre-registration
0.7193 Intermediate Similarity NPD6927 Phase 3
0.6923 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6615 Remote Similarity NPD4191 Approved
0.6615 Remote Similarity NPD4193 Approved
0.6615 Remote Similarity NPD4192 Approved
0.6615 Remote Similarity NPD4194 Approved
0.6567 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6282 Remote Similarity NPD5209 Approved
0.6216 Remote Similarity NPD8039 Approved
0.614 Remote Similarity NPD6097 Approved
0.614 Remote Similarity NPD6096 Approved
0.6102 Remote Similarity NPD5343 Approved
0.6034 Remote Similarity NPD3174 Discontinued
0.6034 Remote Similarity NPD39 Approved
0.597 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5875 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5844 Remote Similarity NPD4756 Discovery
0.5806 Remote Similarity NPD28 Approved
0.5806 Remote Similarity NPD29 Approved
0.5781 Remote Similarity NPD539 Approved
0.5763 Remote Similarity NPD4222 Approved
0.5741 Remote Similarity NPD9115 Approved
0.5738 Remote Similarity NPD3173 Approved
0.5732 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5698 Remote Similarity NPD7838 Discovery
0.569 Remote Similarity NPD9411 Phase 1
0.569 Remote Similarity NPD5326 Phase 3
0.5652 Remote Similarity NPD9418 Clinical (unspecified phase)
0.5625 Remote Similarity NPD3172 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