Structure

Physi-Chem Properties

Molecular Weight:  254.19
Volume:  268.698
LogP:  2.452
LogD:  2.591
LogS:  -2.345
# Rotatable Bonds:  2
TPSA:  52.99
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.741
Synthetic Accessibility Score:  4.498
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:  -4.509
MDCK Permeability:  1.1382913726265542e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.702
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.355
Plasma Protein Binding (PPB):  73.238037109375%
Volume Distribution (VD):  1.056
Pgp-substrate:  22.3822078704834%

ADMET: Metabolism

CYP1A2-inhibitor:  0.06
CYP1A2-substrate:  0.646
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.834
CYP2C9-inhibitor:  0.028
CYP2C9-substrate:  0.042
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.167
CYP3A4-inhibitor:  0.17
CYP3A4-substrate:  0.376

ADMET: Excretion

Clearance (CL):  13.119
Half-life (T1/2):  0.684

ADMET: Toxicity

hERG Blockers:  0.052
Human Hepatotoxicity (H-HT):  0.368
Drug-inuced Liver Injury (DILI):  0.028
AMES Toxicity:  0.04
Rat Oral Acute Toxicity:  0.734
Maximum Recommended Daily Dose:  0.024
Skin Sensitization:  0.688
Carcinogencity:  0.272
Eye Corrosion:  0.558
Eye Irritation:  0.288
Respiratory Toxicity:  0.971

Download Data

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

  Natural Product: NPC199937

Natural Product ID:  NPC199937
Common Name*:   Saniculamoid B
IUPAC Name:   (1aS,4S,4aS,7R,7aR,7bS)-1a-(hydroxymethyl)-4a-methyl-7-propan-2-yl-2,3,4,5,6,7,7a,7b-octahydroazuleno[4,5-b]oxiren-4-ol
Synonyms:   Saniculamoid B
Standard InCHIKey:  WAYKLJZCQJLECB-DBWOOVFOSA-N
Standard InCHI:  InChI=1S/C15H26O3/c1-9(2)10-4-6-14(3)11(17)5-7-15(8-16)13(18-15)12(10)14/h9-13,16-17H,4-8H2,1-3H3/t10-,11+,12+,13+,14-,15+/m1/s1
SMILES:  CC(C)[C@H]1CC[C@]2(C)[C@H](CC[C@]3(CO)[C@H]([C@H]12)O3)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1814424
PubChem CID:   56665185
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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[524906]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 64400.0 nM PMID[524906]
NPT81 Cell Line A549 Homo sapiens IC50 > 64400.0 nM PMID[524906]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 > 64400.0 nM PMID[524906]
NPT116 Cell Line HL-60 Homo sapiens IC50 > 64400.0 nM PMID[524906]
NPT113 Cell Line RAW264.7 Mus musculus IC50 > 64400.0 nM PMID[524906]
NPT1452 Cell Line C8166 Homo sapiens CC50 = 357900.0 nM PMID[524906]
NPT27 Others Unspecified Ratio CC50/EC50 = 2.9 n.a. PMID[524906]
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 EC50 = 125600.0 nM PMID[524906]

☑ 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 NPC199937 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
0.8889 High Similarity NPC165069
0.8387 Intermediate Similarity NPC475968
0.8065 Intermediate Similarity NPC291147
0.8065 Intermediate Similarity NPC119425
0.8056 Intermediate Similarity NPC188793
0.7969 Intermediate Similarity NPC475412
0.7879 Intermediate Similarity NPC476702
0.7867 Intermediate Similarity NPC473257
0.7846 Intermediate Similarity NPC172622
0.7846 Intermediate Similarity NPC475807
0.7742 Intermediate Similarity NPC45387
0.7733 Intermediate Similarity NPC117137
0.7733 Intermediate Similarity NPC66766
0.7632 Intermediate Similarity NPC216941
0.7532 Intermediate Similarity NPC475849
0.75 Intermediate Similarity NPC16449
0.7436 Intermediate Similarity NPC474266
0.7391 Intermediate Similarity NPC469328
0.7333 Intermediate Similarity NPC127997
0.7333 Intermediate Similarity NPC95969
0.7308 Intermediate Similarity NPC212340
0.7297 Intermediate Similarity NPC131584
0.7297 Intermediate Similarity NPC472950
0.7297 Intermediate Similarity NPC139765
0.7297 Intermediate Similarity NPC472952
0.726 Intermediate Similarity NPC470660
0.726 Intermediate Similarity NPC470659
0.7246 Intermediate Similarity NPC472946
0.7231 Intermediate Similarity NPC322148
0.7215 Intermediate Similarity NPC260852
0.72 Intermediate Similarity NPC470145
0.7162 Intermediate Similarity NPC472944
0.7162 Intermediate Similarity NPC472945
0.716 Intermediate Similarity NPC64862
0.7143 Intermediate Similarity NPC81074
0.7143 Intermediate Similarity NPC477282
0.7123 Intermediate Similarity NPC8004
0.7123 Intermediate Similarity NPC127283
0.7105 Intermediate Similarity NPC64081
0.7105 Intermediate Similarity NPC476233
0.7105 Intermediate Similarity NPC11907
0.7105 Intermediate Similarity NPC474574
0.7105 Intermediate Similarity NPC133596
0.7097 Intermediate Similarity NPC474331
0.7089 Intermediate Similarity NPC475388
0.7067 Intermediate Similarity NPC231680
0.7067 Intermediate Similarity NPC91387
0.7067 Intermediate Similarity NPC270306
0.7059 Intermediate Similarity NPC185547
0.7059 Intermediate Similarity NPC95804
0.7042 Intermediate Similarity NPC161612
0.7042 Intermediate Similarity NPC33583
0.7027 Intermediate Similarity NPC476709
0.7013 Intermediate Similarity NPC471769
0.7 Intermediate Similarity NPC29342
0.7 Intermediate Similarity NPC2572
0.6974 Remote Similarity NPC279575
0.6951 Remote Similarity NPC472745
0.6933 Remote Similarity NPC470151
0.6933 Remote Similarity NPC470630
0.6933 Remote Similarity NPC10476
0.6933 Remote Similarity NPC192501
0.6933 Remote Similarity NPC228994
0.6923 Remote Similarity NPC170595
0.6914 Remote Similarity NPC474156
0.6892 Remote Similarity NPC131506
0.6892 Remote Similarity NPC157777
0.6875 Remote Similarity NPC161473
0.6842 Remote Similarity NPC196136
0.6842 Remote Similarity NPC243027
0.6842 Remote Similarity NPC158208
0.6842 Remote Similarity NPC317242
0.6835 Remote Similarity NPC472943
0.6835 Remote Similarity NPC186588
0.6835 Remote Similarity NPC472951
0.68 Remote Similarity NPC248427
0.68 Remote Similarity NPC472341
0.68 Remote Similarity NPC473238
0.6795 Remote Similarity NPC147993
0.679 Remote Similarity NPC470070
0.6765 Remote Similarity NPC185116
0.6753 Remote Similarity NPC163597
0.6714 Remote Similarity NPC209686
0.6714 Remote Similarity NPC236099
0.6714 Remote Similarity NPC249078
0.6712 Remote Similarity NPC474756
0.6711 Remote Similarity NPC475458
0.6711 Remote Similarity NPC190859
0.6709 Remote Similarity NPC287452
0.6709 Remote Similarity NPC269333
0.6667 Remote Similarity NPC477227
0.6667 Remote Similarity NPC283655
0.6667 Remote Similarity NPC83108
0.6667 Remote Similarity NPC476703
0.6667 Remote Similarity NPC202937
0.6667 Remote Similarity NPC178223
0.6667 Remote Similarity NPC192046
0.6667 Remote Similarity NPC302578
0.6667 Remote Similarity NPC89069
0.6667 Remote Similarity NPC185915
0.6667 Remote Similarity NPC214030
0.6667 Remote Similarity NPC41886
0.6667 Remote Similarity NPC105208
0.6667 Remote Similarity NPC277917
0.6667 Remote Similarity NPC166894
0.6667 Remote Similarity NPC470071
0.6667 Remote Similarity NPC195530
0.6667 Remote Similarity NPC187471
0.6667 Remote Similarity NPC202688
0.6667 Remote Similarity NPC60018
0.6667 Remote Similarity NPC252182
0.6667 Remote Similarity NPC154043
0.6667 Remote Similarity NPC1340
0.6667 Remote Similarity NPC128951
0.6627 Remote Similarity NPC290612
0.6622 Remote Similarity NPC107919
0.6622 Remote Similarity NPC299948
0.6622 Remote Similarity NPC241085
0.6622 Remote Similarity NPC99264
0.6622 Remote Similarity NPC66407
0.6622 Remote Similarity NPC470830
0.6618 Remote Similarity NPC215671
0.6618 Remote Similarity NPC87296
0.6618 Remote Similarity NPC475515
0.6618 Remote Similarity NPC476209
0.6588 Remote Similarity NPC22376
0.6585 Remote Similarity NPC472744
0.6585 Remote Similarity NPC69953
0.6585 Remote Similarity NPC259173
0.6585 Remote Similarity NPC477285
0.6585 Remote Similarity NPC111582
0.6582 Remote Similarity NPC67657
0.6582 Remote Similarity NPC18857
0.6582 Remote Similarity NPC470014
0.6579 Remote Similarity NPC470610
0.6579 Remote Similarity NPC143576
0.6579 Remote Similarity NPC153719
0.6552 Remote Similarity NPC474699
0.6548 Remote Similarity NPC474448
0.6548 Remote Similarity NPC155531
0.6548 Remote Similarity NPC215968
0.6538 Remote Similarity NPC170148
0.6538 Remote Similarity NPC126969
0.6533 Remote Similarity NPC282454
0.6533 Remote Similarity NPC471781
0.6533 Remote Similarity NPC470041
0.6528 Remote Similarity NPC190827
0.6528 Remote Similarity NPC243469
0.6528 Remote Similarity NPC300442
0.6528 Remote Similarity NPC250836
0.6528 Remote Similarity NPC475943
0.6522 Remote Similarity NPC52431
0.6522 Remote Similarity NPC310228
0.6506 Remote Similarity NPC320824
0.6506 Remote Similarity NPC242016
0.6506 Remote Similarity NPC86238
0.65 Remote Similarity NPC245029
0.65 Remote Similarity NPC31302
0.6494 Remote Similarity NPC48795
0.6494 Remote Similarity NPC215030
0.6494 Remote Similarity NPC308489
0.6494 Remote Similarity NPC304499
0.6477 Remote Similarity NPC137461
0.6471 Remote Similarity NPC210658
0.6471 Remote Similarity NPC161928
0.6471 Remote Similarity NPC140446
0.6471 Remote Similarity NPC43912
0.6471 Remote Similarity NPC29976
0.6471 Remote Similarity NPC472396
0.6471 Remote Similarity NPC5943
0.6471 Remote Similarity NPC150713
0.6463 Remote Similarity NPC102156
0.6463 Remote Similarity NPC477286
0.6463 Remote Similarity NPC242771
0.6463 Remote Similarity NPC100366
0.6463 Remote Similarity NPC311642
0.6463 Remote Similarity NPC148740
0.6463 Remote Similarity NPC164289
0.6463 Remote Similarity NPC286719
0.6456 Remote Similarity NPC471454
0.6447 Remote Similarity NPC109457
0.6447 Remote Similarity NPC473279
0.6447 Remote Similarity NPC157422
0.6447 Remote Similarity NPC100586
0.6447 Remote Similarity NPC127094
0.6429 Remote Similarity NPC266651
0.6418 Remote Similarity NPC471269
0.641 Remote Similarity NPC179922
0.641 Remote Similarity NPC186851
0.6404 Remote Similarity NPC30687
0.64 Remote Similarity NPC129829
0.64 Remote Similarity NPC477820
0.64 Remote Similarity NPC470833
0.64 Remote Similarity NPC254037
0.6395 Remote Similarity NPC470009
0.6395 Remote Similarity NPC128475
0.6395 Remote Similarity NPC473436
0.6389 Remote Similarity NPC219940
0.6389 Remote Similarity NPC94897
0.6386 Remote Similarity NPC292458

  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 NPC199937 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
0.7101 Intermediate Similarity NPD371 Approved
0.6622 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6279 Remote Similarity NPD7524 Approved
0.6118 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6032 Remote Similarity NPD386 Approved
0.6032 Remote Similarity NPD388 Approved
0.6024 Remote Similarity NPD6928 Phase 2
0.6 Remote Similarity NPD6695 Phase 3
0.5938 Remote Similarity NPD384 Approved
0.5938 Remote Similarity NPD385 Approved
0.5934 Remote Similarity NPD8171 Discontinued
0.5926 Remote Similarity NPD6933 Approved
0.5897 Remote Similarity NPD7532 Clinical (unspecified phase)
0.5897 Remote Similarity NPD4787 Phase 1
0.5875 Remote Similarity NPD1811 Approved
0.5875 Remote Similarity NPD1810 Approved
0.5867 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6930 Phase 2
0.5833 Remote Similarity NPD6931 Approved
0.573 Remote Similarity NPD7750 Discontinued
0.5714 Remote Similarity NPD6929 Approved
0.5679 Remote Similarity NPD6924 Approved
0.5679 Remote Similarity NPD6926 Approved
0.567 Remote Similarity NPD1700 Approved
0.5663 Remote Similarity NPD6932 Approved
0.5634 Remote Similarity NPD2267 Suspended
0.5625 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5625 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5616 Remote Similarity NPD3198 Approved
0.561 Remote Similarity NPD3702 Approved
0.561 Remote Similarity NPD3703 Phase 2

  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