Structure

Physi-Chem Properties

Molecular Weight:  272.2
Volume:  286.044
LogP:  1.303
LogD:  1.488
LogS:  -1.877
# Rotatable Bonds:  1
TPSA:  80.92
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.575
Synthetic Accessibility Score:  4.607
Fsp3:  1.0
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:  -4.596
MDCK Permeability:  2.0382614820846356e-05
Pgp-inhibitor:  0.129
Pgp-substrate:  0.819
Human Intestinal Absorption (HIA):  0.041
20% Bioavailability (F20%):  0.739
30% Bioavailability (F30%):  0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.892
Plasma Protein Binding (PPB):  33.43720245361328%
Volume Distribution (VD):  1.085
Pgp-substrate:  40.27157211303711%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.217
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.764
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.213
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.065
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.219

ADMET: Excretion

Clearance (CL):  5.9
Half-life (T1/2):  0.61

ADMET: Toxicity

hERG Blockers:  0.058
Human Hepatotoxicity (H-HT):  0.194
Drug-inuced Liver Injury (DILI):  0.058
AMES Toxicity:  0.024
Rat Oral Acute Toxicity:  0.056
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.733
Carcinogencity:  0.547
Eye Corrosion:  0.894
Eye Irritation:  0.975
Respiratory Toxicity:  0.939

Download Data

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

  Natural Product: NPC119425

Natural Product ID:  NPC119425
Common Name*:   Saniculamoid C
IUPAC Name:   (1R,3aS,4R,6S,7S,8aS)-7-(2-hydroxypropan-2-yl)-1,4-dimethyl-2,3,3a,5,6,7,8,8a-octahydroazulene-1,4,6-triol
Synonyms:   Saniculamoid C
Standard InCHIKey:  HASSBFRDJUITDM-OOAGNDBOSA-N
Standard InCHI:  InChI=1S/C15H28O4/c1-13(2,17)11-7-10-9(5-6-14(10,3)18)15(4,19)8-12(11)16/h9-12,16-19H,5-8H2,1-4H3/t9-,10-,11-,12-,14+,15+/m0/s1
SMILES:  CC(C)([C@H]1C[C@H]2[C@H](CC[C@@]2(C)O)[C@@](C)(C[C@@H]1O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1814425
PubChem CID:   53360478
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002874] Guaianes

*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
NPO29956 Sanicula lamelligera Species Apiaceae Eukaryota Whole plants Mountain Emei, Sichuan Province, China 2008-OCT PMID[21561060]
NPO29956 Sanicula lamelligera Species Apiaceae Eukaryota n.a. whole plant n.a. PMID[21561060]

☑ 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
NPT660 Cell Line SW480 Homo sapiens IC50 > 64400.0 nM PMID[505138]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 64400.0 nM PMID[505138]
NPT81 Cell Line A549 Homo sapiens IC50 > 64400.0 nM PMID[505138]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 > 64400.0 nM PMID[505138]
NPT116 Cell Line HL-60 Homo sapiens IC50 > 64400.0 nM PMID[505138]
NPT113 Cell Line RAW264.7 Mus musculus IC50 > 64400.0 nM PMID[505138]
NPT1452 Cell Line C8166 Homo sapiens CC50 > 367600.0 nM PMID[505138]
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 EC50 > 367600.0 nM PMID[505138]

☑ 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 NPC119425 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
0.8621 High Similarity NPC475968
0.8596 High Similarity NPC291147
0.8246 Intermediate Similarity NPC45387
0.8065 Intermediate Similarity NPC199937
0.7937 Intermediate Similarity NPC165069
0.7705 Intermediate Similarity NPC310228
0.7705 Intermediate Similarity NPC52431
0.7681 Intermediate Similarity NPC131584
0.7681 Intermediate Similarity NPC139765
0.7538 Intermediate Similarity NPC469328
0.7344 Intermediate Similarity NPC236099
0.7344 Intermediate Similarity NPC249078
0.7344 Intermediate Similarity NPC209686
0.7333 Intermediate Similarity NPC277917
0.7333 Intermediate Similarity NPC283655
0.7333 Intermediate Similarity NPC89069
0.7333 Intermediate Similarity NPC178223
0.7333 Intermediate Similarity NPC166894
0.7313 Intermediate Similarity NPC474756
0.7286 Intermediate Similarity NPC304499
0.7286 Intermediate Similarity NPC475458
0.7193 Intermediate Similarity NPC127997
0.7193 Intermediate Similarity NPC95969
0.7183 Intermediate Similarity NPC317242
0.7162 Intermediate Similarity NPC117137
0.7162 Intermediate Similarity NPC66766
0.7143 Intermediate Similarity NPC470660
0.7143 Intermediate Similarity NPC470659
0.7121 Intermediate Similarity NPC472946
0.7101 Intermediate Similarity NPC470041
0.7101 Intermediate Similarity NPC232925
0.7101 Intermediate Similarity NPC63588
0.7101 Intermediate Similarity NPC471781
0.7101 Intermediate Similarity NPC251201
0.7097 Intermediate Similarity NPC150713
0.7097 Intermediate Similarity NPC29976
0.7083 Intermediate Similarity NPC279575
0.7083 Intermediate Similarity NPC163597
0.7067 Intermediate Similarity NPC473257
0.7027 Intermediate Similarity NPC170595
0.6986 Remote Similarity NPC192046
0.6986 Remote Similarity NPC477227
0.6986 Remote Similarity NPC128951
0.6986 Remote Similarity NPC214030
0.6986 Remote Similarity NPC188793
0.6986 Remote Similarity NPC83108
0.6986 Remote Similarity NPC185915
0.6986 Remote Similarity NPC302578
0.6986 Remote Similarity NPC105208
0.697 Remote Similarity NPC476702
0.6957 Remote Similarity NPC66407
0.6957 Remote Similarity NPC477820
0.6923 Remote Similarity NPC172622
0.6923 Remote Similarity NPC63111
0.6923 Remote Similarity NPC185547
0.6923 Remote Similarity NPC95804
0.6901 Remote Similarity NPC470610
0.6901 Remote Similarity NPC153719
0.6901 Remote Similarity NPC248427
0.6892 Remote Similarity NPC67657
0.6892 Remote Similarity NPC18857
0.6883 Remote Similarity NPC29342
0.6883 Remote Similarity NPC2572
0.6866 Remote Similarity NPC469326
0.6866 Remote Similarity NPC261782
0.6866 Remote Similarity NPC205618
0.6857 Remote Similarity NPC133873
0.6825 Remote Similarity NPC322148
0.6812 Remote Similarity NPC319007
0.6806 Remote Similarity NPC48795
0.6806 Remote Similarity NPC215030
0.68 Remote Similarity NPC287452
0.68 Remote Similarity NPC269333
0.6795 Remote Similarity NPC242016
0.6769 Remote Similarity NPC475412
0.6761 Remote Similarity NPC41886
0.6761 Remote Similarity NPC252182
0.6761 Remote Similarity NPC1340
0.6761 Remote Similarity NPC187471
0.6761 Remote Similarity NPC127094
0.6761 Remote Similarity NPC470071
0.6757 Remote Similarity NPC476233
0.6721 Remote Similarity NPC161473
0.6719 Remote Similarity NPC87296
0.6719 Remote Similarity NPC475515
0.6719 Remote Similarity NPC215671
0.6714 Remote Similarity NPC475062
0.6714 Remote Similarity NPC98711
0.6714 Remote Similarity NPC144647
0.6712 Remote Similarity NPC243027
0.6712 Remote Similarity NPC158208
0.6712 Remote Similarity NPC196136
0.6667 Remote Similarity NPC77550
0.6667 Remote Similarity NPC108441
0.6667 Remote Similarity NPC472253
0.6667 Remote Similarity NPC472255
0.6667 Remote Similarity NPC307022
0.6667 Remote Similarity NPC471045
0.6667 Remote Similarity NPC475807
0.6667 Remote Similarity NPC111409
0.6625 Remote Similarity NPC145245
0.6623 Remote Similarity NPC216941
0.6622 Remote Similarity NPC126969
0.662 Remote Similarity NPC254845
0.662 Remote Similarity NPC192192
0.6618 Remote Similarity NPC300442
0.6618 Remote Similarity NPC475943
0.6618 Remote Similarity NPC190827
0.6618 Remote Similarity NPC243469
0.6615 Remote Similarity NPC184049
0.6615 Remote Similarity NPC99480
0.6607 Remote Similarity NPC144891
0.6582 Remote Similarity NPC16887
0.6582 Remote Similarity NPC37005
0.6582 Remote Similarity NPC154893
0.6582 Remote Similarity NPC53011
0.6575 Remote Similarity NPC192501
0.6575 Remote Similarity NPC10476
0.6575 Remote Similarity NPC470630
0.6575 Remote Similarity NPC228994
0.6552 Remote Similarity NPC287550
0.6552 Remote Similarity NPC147343
0.6552 Remote Similarity NPC84030
0.6552 Remote Similarity NPC176309
0.6552 Remote Similarity NPC223468
0.6552 Remote Similarity NPC198540
0.6538 Remote Similarity NPC475388
0.6538 Remote Similarity NPC475849
0.6538 Remote Similarity NPC212340
0.6533 Remote Similarity NPC70996
0.6522 Remote Similarity NPC44122
0.6522 Remote Similarity NPC272125
0.6508 Remote Similarity NPC471269
0.6494 Remote Similarity NPC474714
0.6491 Remote Similarity NPC240994
0.6486 Remote Similarity NPC35871
0.6486 Remote Similarity NPC68565
0.6479 Remote Similarity NPC107919
0.6479 Remote Similarity NPC129829
0.6479 Remote Similarity NPC99264
0.6479 Remote Similarity NPC254037
0.6471 Remote Similarity NPC219940
0.6471 Remote Similarity NPC118937
0.6471 Remote Similarity NPC281540
0.6471 Remote Similarity NPC167995
0.6471 Remote Similarity NPC159654
0.6471 Remote Similarity NPC94897
0.6463 Remote Similarity NPC22376
0.6456 Remote Similarity NPC474266
0.6456 Remote Similarity NPC69953
0.6456 Remote Similarity NPC478054
0.6456 Remote Similarity NPC232023
0.6447 Remote Similarity NPC147993
0.6438 Remote Similarity NPC310608
0.6438 Remote Similarity NPC476422
0.6429 Remote Similarity NPC63190
0.642 Remote Similarity NPC64862
0.6415 Remote Similarity NPC177022
0.641 Remote Similarity NPC254123
0.6406 Remote Similarity NPC3025
0.6386 Remote Similarity NPC215556
0.6377 Remote Similarity NPC238352
0.6377 Remote Similarity NPC477009
0.6375 Remote Similarity NPC474156
0.6364 Remote Similarity NPC81074
0.6364 Remote Similarity NPC477282
0.6364 Remote Similarity NPC476176
0.6351 Remote Similarity NPC472944
0.6351 Remote Similarity NPC472945
0.6351 Remote Similarity NPC471659
0.6338 Remote Similarity NPC167527
0.6338 Remote Similarity NPC472741
0.6338 Remote Similarity NPC224532
0.6324 Remote Similarity NPC114891
0.6316 Remote Similarity NPC64081
0.6316 Remote Similarity NPC133596
0.6316 Remote Similarity NPC11907
0.6316 Remote Similarity NPC474574
0.631 Remote Similarity NPC216284
0.6301 Remote Similarity NPC157422
0.6301 Remote Similarity NPC109457
0.6301 Remote Similarity NPC100586
0.6296 Remote Similarity NPC266651
0.6282 Remote Similarity NPC78545
0.6282 Remote Similarity NPC71535
0.6282 Remote Similarity NPC258965
0.6282 Remote Similarity NPC156658
0.6267 Remote Similarity NPC179922
0.6265 Remote Similarity NPC79549
0.625 Remote Similarity NPC260852
0.625 Remote Similarity NPC470833
0.625 Remote Similarity NPC128246
0.625 Remote Similarity NPC474900
0.625 Remote Similarity NPC157328
0.6234 Remote Similarity NPC471769
0.6234 Remote Similarity NPC477819
0.6234 Remote Similarity NPC477817
0.6226 Remote Similarity NPC328441
0.622 Remote Similarity NPC470657
0.622 Remote Similarity NPC6605

  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 NPC119425 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
0.6667 Remote Similarity NPD388 Approved
0.6667 Remote Similarity NPD386 Approved
0.6615 Remote Similarity NPD3198 Approved
0.6552 Remote Similarity NPD385 Approved
0.6552 Remote Similarity NPD384 Approved
0.6479 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6471 Remote Similarity NPD371 Approved
0.6389 Remote Similarity NPD4787 Phase 1
0.614 Remote Similarity NPD1462 Approved
0.6076 Remote Similarity NPD6928 Phase 2
0.6071 Remote Similarity NPD1460 Approved
0.6027 Remote Similarity NPD3698 Phase 2
0.5976 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5946 Remote Similarity NPD4244 Approved
0.5946 Remote Similarity NPD4245 Approved
0.5915 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5875 Remote Similarity NPD4821 Approved
0.5875 Remote Similarity NPD4819 Approved
0.5875 Remote Similarity NPD4822 Approved
0.5875 Remote Similarity NPD6930 Phase 2
0.5875 Remote Similarity NPD6931 Approved
0.5875 Remote Similarity NPD4820 Approved
0.5854 Remote Similarity NPD6695 Phase 3
0.5823 Remote Similarity NPD6115 Approved
0.5823 Remote Similarity NPD4802 Phase 2
0.5823 Remote Similarity NPD6697 Approved
0.5823 Remote Similarity NPD6114 Approved
0.5823 Remote Similarity NPD6118 Approved
0.5823 Remote Similarity NPD4238 Approved
0.575 Remote Similarity NPD6929 Approved
0.5714 Remote Similarity NPD1810 Approved
0.5714 Remote Similarity NPD6926 Approved
0.5714 Remote Similarity NPD6924 Approved
0.5714 Remote Similarity NPD1811 Approved
0.5696 Remote Similarity NPD6116 Phase 1
0.5696 Remote Similarity NPD6932 Approved
0.5679 Remote Similarity NPD4748 Discontinued
0.5679 Remote Similarity NPD5368 Approved
0.5679 Remote Similarity NPD7525 Registered
0.5672 Remote Similarity NPD586 Phase 1
0.5658 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5658 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5641 Remote Similarity NPD3702 Approved
0.5641 Remote Similarity NPD3703 Phase 2
0.5625 Remote Similarity NPD4268 Approved
0.5625 Remote Similarity NPD4271 Approved
0.5618 Remote Similarity NPD8171 Discontinued
0.56 Remote Similarity NPD3700 Clinical (unspecified phase)
0.56 Remote Similarity NPD3699 Clinical (unspecified phase)

  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