Structure

Physi-Chem Properties

Molecular Weight:  228.1
Volume:  220.378
LogP:  1.392
LogD:  1.109
LogS:  -3.084
# Rotatable Bonds:  2
TPSA:  65.13
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.487
Synthetic Accessibility Score:  5.01
Fsp3:  0.818
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.188
MDCK Permeability:  3.2293650292558596e-05
Pgp-inhibitor:  0.438
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.016
30% Bioavailability (F30%):  0.099

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.975
Plasma Protein Binding (PPB):  34.770687103271484%
Volume Distribution (VD):  1.008
Pgp-substrate:  69.0423583984375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.035
CYP1A2-substrate:  0.935
CYP2C19-inhibitor:  0.158
CYP2C19-substrate:  0.876
CYP2C9-inhibitor:  0.023
CYP2C9-substrate:  0.081
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.362
CYP3A4-inhibitor:  0.144
CYP3A4-substrate:  0.552

ADMET: Excretion

Clearance (CL):  6.813
Half-life (T1/2):  0.813

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.877
Drug-inuced Liver Injury (DILI):  0.931
AMES Toxicity:  0.887
Rat Oral Acute Toxicity:  0.233
Maximum Recommended Daily Dose:  0.042
Skin Sensitization:  0.585
Carcinogencity:  0.757
Eye Corrosion:  0.039
Eye Irritation:  0.494
Respiratory Toxicity:  0.018

Download Data

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

  Natural Product: NPC96322

Natural Product ID:  NPC96322
Common Name*:   Liguhodgcins B
IUPAC Name:   methyl (2R,3R,5R,6R)-2,5,6-trimethyl-8-oxo-1,7-dioxaspiro[2.5]octane-6-carboxylate
Synonyms:   Liguhodgcins B
Standard InCHIKey:  COYQJFOFZGEQLA-JJHYMCDRSA-N
Standard InCHI:  InChI=1S/C11H16O5/c1-6-5-11(7(2)15-11)9(13)16-10(6,3)8(12)14-4/h6-7H,5H2,1-4H3/t6-,7-,10-,11-/m1/s1
SMILES:  C[C@@H]1C[C@@]2([C@@H](C)O2)C(=O)O[C@@]1(C)C(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2062983
PubChem CID:   60154790
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001244] Delta valerolactones

*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
NPO18454 Ligularia hodgsonii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22642381]
NPO18454 Ligularia hodgsonii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ 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
NPT116 Cell Line HL-60 Homo sapiens IC50 = 151400.0 nM PMID[545069]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 = 162200.0 nM PMID[545069]
NPT165 Cell Line HeLa Homo sapiens IC50 = 168400.0 nM PMID[545069]

☑ 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 NPC96322 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
0.8267 Intermediate Similarity NPC108014
0.7973 Intermediate Similarity NPC470526
0.7792 Intermediate Similarity NPC474003
0.7674 Intermediate Similarity NPC474379
0.759 Intermediate Similarity NPC475491
0.759 Intermediate Similarity NPC469626
0.7468 Intermediate Similarity NPC470014
0.7429 Intermediate Similarity NPC472021
0.7342 Intermediate Similarity NPC83108
0.7342 Intermediate Similarity NPC214030
0.7286 Intermediate Similarity NPC472020
0.7286 Intermediate Similarity NPC226602
0.7286 Intermediate Similarity NPC472019
0.726 Intermediate Similarity NPC469926
0.7241 Intermediate Similarity NPC65359
0.7229 Intermediate Similarity NPC476721
0.7195 Intermediate Similarity NPC329490
0.7195 Intermediate Similarity NPC328639
0.7179 Intermediate Similarity NPC477867
0.7176 Intermediate Similarity NPC477441
0.7159 Intermediate Similarity NPC216137
0.7159 Intermediate Similarity NPC469627
0.7143 Intermediate Similarity NPC475689
0.7111 Intermediate Similarity NPC470191
0.7105 Intermediate Similarity NPC98711
0.7083 Intermediate Similarity NPC469923
0.7083 Intermediate Similarity NPC469922
0.7067 Intermediate Similarity NPC286842
0.7042 Intermediate Similarity NPC475821
0.7027 Intermediate Similarity NPC215987
0.7027 Intermediate Similarity NPC306805
0.6986 Remote Similarity NPC474552
0.6977 Remote Similarity NPC476717
0.6947 Remote Similarity NPC469350
0.6923 Remote Similarity NPC322188
0.6914 Remote Similarity NPC143250
0.6897 Remote Similarity NPC314364
0.6883 Remote Similarity NPC475062
0.6875 Remote Similarity NPC471491
0.6854 Remote Similarity NPC477444
0.6854 Remote Similarity NPC477442
0.6854 Remote Similarity NPC477433
0.6806 Remote Similarity NPC469924
0.679 Remote Similarity NPC474020
0.6786 Remote Similarity NPC207188
0.6782 Remote Similarity NPC474215
0.6782 Remote Similarity NPC475729
0.6782 Remote Similarity NPC470657
0.6778 Remote Similarity NPC474699
0.6757 Remote Similarity NPC235788
0.675 Remote Similarity NPC215030
0.675 Remote Similarity NPC125164
0.6747 Remote Similarity NPC275243
0.6747 Remote Similarity NPC276647
0.6747 Remote Similarity NPC622
0.6744 Remote Similarity NPC65133
0.6742 Remote Similarity NPC477443
0.6742 Remote Similarity NPC477440
0.6742 Remote Similarity NPC475971
0.6737 Remote Similarity NPC162024
0.6737 Remote Similarity NPC471767
0.6711 Remote Similarity NPC241949
0.6709 Remote Similarity NPC470243
0.6706 Remote Similarity NPC248415
0.6705 Remote Similarity NPC31349
0.6702 Remote Similarity NPC253995
0.6702 Remote Similarity NPC274695
0.6667 Remote Similarity NPC17585
0.6667 Remote Similarity NPC476715
0.6667 Remote Similarity NPC125366
0.6667 Remote Similarity NPC477264
0.6667 Remote Similarity NPC250594
0.6667 Remote Similarity NPC477205
0.6667 Remote Similarity NPC60568
0.6667 Remote Similarity NPC51267
0.6633 Remote Similarity NPC474101
0.6633 Remote Similarity NPC314244
0.6628 Remote Similarity NPC257358
0.6628 Remote Similarity NPC474472
0.6623 Remote Similarity NPC469925
0.66 Remote Similarity NPC474242
0.6593 Remote Similarity NPC20713
0.6593 Remote Similarity NPC329952
0.6591 Remote Similarity NPC235196
0.6591 Remote Similarity NPC228593
0.6588 Remote Similarity NPC285480
0.6588 Remote Similarity NPC30443
0.6588 Remote Similarity NPC45256
0.6588 Remote Similarity NPC260977
0.6579 Remote Similarity NPC476330
0.6566 Remote Similarity NPC137453
0.6562 Remote Similarity NPC477511
0.6562 Remote Similarity NPC201718
0.6562 Remote Similarity NPC259654
0.6562 Remote Similarity NPC298266
0.6562 Remote Similarity NPC264477
0.6559 Remote Similarity NPC475900
0.6552 Remote Similarity NPC471343
0.6552 Remote Similarity NPC115995
0.6552 Remote Similarity NPC477434
0.6528 Remote Similarity NPC220922
0.6522 Remote Similarity NPC228700
0.6517 Remote Similarity NPC5130
0.6517 Remote Similarity NPC51662
0.6517 Remote Similarity NPC197333
0.6517 Remote Similarity NPC471739
0.6512 Remote Similarity NPC212340
0.6506 Remote Similarity NPC70996
0.65 Remote Similarity NPC153587
0.6489 Remote Similarity NPC476009
0.6486 Remote Similarity NPC469921
0.6484 Remote Similarity NPC246173
0.6477 Remote Similarity NPC47958
0.6477 Remote Similarity NPC149725
0.6477 Remote Similarity NPC304509
0.6477 Remote Similarity NPC478111
0.6471 Remote Similarity NPC134227
0.6463 Remote Similarity NPC228411
0.6463 Remote Similarity NPC179922
0.6458 Remote Similarity NPC469551
0.6458 Remote Similarity NPC477512
0.6452 Remote Similarity NPC309127
0.6452 Remote Similarity NPC477495
0.6452 Remote Similarity NPC247877
0.6444 Remote Similarity NPC221993
0.6444 Remote Similarity NPC476379
0.6444 Remote Similarity NPC236459
0.6444 Remote Similarity NPC471221
0.6438 Remote Similarity NPC179624
0.6437 Remote Similarity NPC227170
0.6437 Remote Similarity NPC157328
0.6436 Remote Similarity NPC204652
0.6436 Remote Similarity NPC16657
0.6429 Remote Similarity NPC19239
0.6429 Remote Similarity NPC475725
0.6429 Remote Similarity NPC474166
0.6421 Remote Similarity NPC266417
0.6421 Remote Similarity NPC236176
0.6421 Remote Similarity NPC471140
0.642 Remote Similarity NPC474755
0.642 Remote Similarity NPC123122
0.641 Remote Similarity NPC57788
0.641 Remote Similarity NPC53879
0.641 Remote Similarity NPC32148
0.6408 Remote Similarity NPC98870
0.64 Remote Similarity NPC469558
0.64 Remote Similarity NPC474716
0.64 Remote Similarity NPC469788
0.64 Remote Similarity NPC469787
0.64 Remote Similarity NPC290247
0.64 Remote Similarity NPC253204
0.6386 Remote Similarity NPC474316
0.6386 Remote Similarity NPC476985
0.6386 Remote Similarity NPC475744
0.6377 Remote Similarity NPC287811
0.6377 Remote Similarity NPC314084
0.6374 Remote Similarity NPC151770
0.6364 Remote Similarity NPC474741
0.6364 Remote Similarity NPC471143
0.6364 Remote Similarity NPC138647
0.6364 Remote Similarity NPC32565
0.6364 Remote Similarity NPC120726
0.6364 Remote Similarity NPC470238
0.6364 Remote Similarity NPC477510
0.6354 Remote Similarity NPC208233
0.6353 Remote Similarity NPC471740
0.6351 Remote Similarity NPC470363
0.6344 Remote Similarity NPC475788
0.6341 Remote Similarity NPC55508
0.6341 Remote Similarity NPC330016
0.6337 Remote Similarity NPC117604
0.6337 Remote Similarity NPC329876
0.6333 Remote Similarity NPC231889
0.6333 Remote Similarity NPC470920
0.6327 Remote Similarity NPC49393
0.6327 Remote Similarity NPC105725
0.6316 Remote Similarity NPC470883
0.6316 Remote Similarity NPC235109
0.6316 Remote Similarity NPC158416
0.6316 Remote Similarity NPC476275
0.6316 Remote Similarity NPC325773
0.6316 Remote Similarity NPC469369
0.6316 Remote Similarity NPC469528
0.6316 Remote Similarity NPC317651
0.6316 Remote Similarity NPC39859
0.6316 Remote Similarity NPC258690
0.6316 Remote Similarity NPC76862
0.6304 Remote Similarity NPC475748
0.6304 Remote Similarity NPC329857
0.6304 Remote Similarity NPC469718
0.63 Remote Similarity NPC475802
0.63 Remote Similarity NPC16313
0.63 Remote Similarity NPC9303
0.6292 Remote Similarity NPC473350
0.6289 Remote Similarity NPC475949
0.6286 Remote Similarity NPC470115
0.6286 Remote Similarity NPC470116
0.6279 Remote Similarity NPC1882
0.6279 Remote Similarity NPC103634
0.6279 Remote Similarity NPC474981

  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 NPC96322 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
0.6915 Remote Similarity NPD1700 Approved
0.6842 Remote Similarity NPD8301 Approved
0.6842 Remote Similarity NPD8300 Approved
0.6588 Remote Similarity NPD1780 Approved
0.6588 Remote Similarity NPD1779 Approved
0.6528 Remote Similarity NPD8959 Approved
0.641 Remote Similarity NPD897 Approved
0.641 Remote Similarity NPD898 Approved
0.641 Remote Similarity NPD896 Approved
0.6316 Remote Similarity NPD8961 Approved
0.6235 Remote Similarity NPD4238 Approved
0.6235 Remote Similarity NPD4802 Phase 2
0.62 Remote Similarity NPD4057 Clinical (unspecified phase)
0.62 Remote Similarity NPD4056 Clinical (unspecified phase)
0.6176 Remote Similarity NPD5345 Clinical (unspecified phase)
0.6176 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6164 Remote Similarity NPD73 Approved
0.6154 Remote Similarity NPD9496 Clinical (unspecified phase)
0.6125 Remote Similarity NPD229 Approved
0.6111 Remote Similarity NPD1733 Clinical (unspecified phase)
0.6026 Remote Similarity NPD7909 Approved
0.6 Remote Similarity NPD8084 Approved
0.6 Remote Similarity NPD8086 Approved
0.6 Remote Similarity NPD8085 Approved
0.6 Remote Similarity NPD8082 Approved
0.6 Remote Similarity NPD8139 Approved
0.6 Remote Similarity NPD8138 Approved
0.6 Remote Similarity NPD8083 Approved
0.5977 Remote Similarity NPD7329 Approved
0.5957 Remote Similarity NPD46 Approved
0.5957 Remote Similarity NPD6698 Approved
0.5955 Remote Similarity NPD7345 Approved
0.5941 Remote Similarity NPD8276 Approved
0.5941 Remote Similarity NPD8275 Approved
0.5895 Remote Similarity NPD7983 Approved
0.5882 Remote Similarity NPD8081 Approved
0.5833 Remote Similarity NPD9007 Approved
0.5833 Remote Similarity NPD64 Approved
0.5833 Remote Similarity NPD8960 Approved
0.5833 Remote Similarity NPD65 Approved
0.5833 Remote Similarity NPD66 Approved
0.5833 Remote Similarity NPD9008 Approved
0.5833 Remote Similarity NPD9009 Approved
0.5833 Remote Similarity NPD9010 Approved
0.5833 Remote Similarity NPD72 Approved
0.5833 Remote Similarity NPD9011 Approved
0.5825 Remote Similarity NPD8393 Approved
0.5773 Remote Similarity NPD5282 Discontinued
0.5769 Remote Similarity NPD8140 Approved
0.5769 Remote Similarity NPD8307 Discontinued
0.5727 Remote Similarity NPD8295 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3670 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3669 Approved
0.5698 Remote Similarity NPD11 Approved
0.5698 Remote Similarity NPD376 Approved
0.5698 Remote Similarity NPD3702 Approved
0.5694 Remote Similarity NPD1400 Approved
0.5694 Remote Similarity NPD1399 Approved
0.5684 Remote Similarity NPD6101 Approved
0.5684 Remote Similarity NPD1695 Approved
0.5684 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5676 Remote Similarity NPD3728 Approved
0.5676 Remote Similarity NPD3730 Approved
0.567 Remote Similarity NPD5778 Approved
0.567 Remote Similarity NPD5779 Approved
0.566 Remote Similarity NPD8306 Approved
0.566 Remote Similarity NPD8305 Approved
0.5647 Remote Similarity NPD3181 Approved
0.5625 Remote Similarity NPD371 Approved
0.5619 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5607 Remote Similarity NPD8087 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