Structure

Physi-Chem Properties

Molecular Weight:  560.23
Volume:  527.835
LogP:  1.622
LogD:  0.788
LogS:  -4.301
# Rotatable Bonds:  1
TPSA:  154.89
# H-Bond Aceptor:  11
# H-Bond Donor:  2
# Rings:  8
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.441
Synthetic Accessibility Score:  7.733
Fsp3:  0.862
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.405
MDCK Permeability:  4.263366281520575e-05
Pgp-inhibitor:  0.794
Pgp-substrate:  0.559
Human Intestinal Absorption (HIA):  0.043
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.93

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.679
Plasma Protein Binding (PPB):  44.426185607910156%
Volume Distribution (VD):  0.583
Pgp-substrate:  46.234031677246094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.996
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.503
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.002
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.024
CYP3A4-inhibitor:  0.933
CYP3A4-substrate:  0.931

ADMET: Excretion

Clearance (CL):  11.276
Half-life (T1/2):  0.159

ADMET: Toxicity

hERG Blockers:  0.05
Human Hepatotoxicity (H-HT):  0.498
Drug-inuced Liver Injury (DILI):  0.9
AMES Toxicity:  0.95
Rat Oral Acute Toxicity:  0.983
Maximum Recommended Daily Dose:  0.948
Skin Sensitization:  0.81
Carcinogencity:  0.938
Eye Corrosion:  0.014
Eye Irritation:  0.012
Respiratory Toxicity:  0.981

Download Data

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

  Natural Product: NPC41674

Natural Product ID:  NPC41674
Common Name*:   Schirubridilactone C
IUPAC Name:   n.a.
Synonyms:   Schirubridilactone C
Standard InCHIKey:  KWZAQNBIRDZLHQ-AIIWDFQCSA-N
Standard InCHI:  InChI=1S/C29H36O11/c1-13-10-28(38-21(13)33)18-14(2)20(32)23(3)7-8-25-11-26-15(24(4,12-30)36-16(26)9-17(31)37-26)5-6-27(25,35)22(34)29(39-25,40-28)19(18)23/h13-16,18-19,30,35H,5-12H2,1-4H3/t13-,14-,15-,16+,18-,19-,23-,24-,25-,26+,27+,28+,29+/m0/s1
SMILES:  OC[C@]1(C)O[C@H]2[C@@]3([C@H]1CC[C@@]1([C@@]4(C3)CC[C@]3([C@H]5[C@@](C1=O)(O4)O[C@]1([C@H]5[C@@H](C3=O)C)OC(=O)[C@H](C1)C)C)O)OC(=O)C2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1076666
PubChem CID:   46186628
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000513] Eicosanoids
          • [CHEMONTID:0000514] Prostaglandins and related compounds

*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
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. stem n.a. PMID[16494492]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. leaf n.a. PMID[16494492]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. fruit n.a. PMID[17190445]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[17190445]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[17489633]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota leaves and stems n.a. n.a. PMID[20146529]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24804 Schisandra rubriflora Species Schisandraceae 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
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 EC50 = 14.3 ug.mL-1 PMID[507583]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Selectivity Index = 8.7 n.a. PMID[507583]

☑ 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 NPC41674 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
1.0 High Similarity NPC228311
1.0 High Similarity NPC469441
0.9798 High Similarity NPC329876
0.9697 High Similarity NPC469787
0.9697 High Similarity NPC290247
0.9697 High Similarity NPC469788
0.96 High Similarity NPC278693
0.96 High Similarity NPC220773
0.9505 High Similarity NPC217041
0.9412 High Similarity NPC182185
0.94 High Similarity NPC168890
0.9231 High Similarity NPC98870
0.9118 High Similarity NPC176756
0.9029 High Similarity NPC167044
0.901 High Similarity NPC469350
0.899 High Similarity NPC274695
0.8812 High Similarity NPC162024
0.8558 High Similarity NPC88890
0.8558 High Similarity NPC18044
0.8558 High Similarity NPC169089
0.8558 High Similarity NPC132304
0.8558 High Similarity NPC177518
0.8558 High Similarity NPC123070
0.8558 High Similarity NPC154962
0.8558 High Similarity NPC114365
0.8558 High Similarity NPC18433
0.8365 Intermediate Similarity NPC292803
0.8155 Intermediate Similarity NPC278028
0.8155 Intermediate Similarity NPC328180
0.8103 Intermediate Similarity NPC186339
0.7949 Intermediate Similarity NPC1538
0.7899 Intermediate Similarity NPC11732
0.7869 Intermediate Similarity NPC224623
0.7863 Intermediate Similarity NPC192309
0.7769 Intermediate Similarity NPC13071
0.7706 Intermediate Similarity NPC473701
0.7706 Intermediate Similarity NPC473526
0.7705 Intermediate Similarity NPC469351
0.7686 Intermediate Similarity NPC172823
0.7647 Intermediate Similarity NPC42747
0.7583 Intermediate Similarity NPC144625
0.75 Intermediate Similarity NPC473791
0.75 Intermediate Similarity NPC475490
0.7451 Intermediate Similarity NPC314364
0.7407 Intermediate Similarity NPC211087
0.7379 Intermediate Similarity NPC470009
0.7321 Intermediate Similarity NPC166079
0.729 Intermediate Similarity NPC470191
0.725 Intermediate Similarity NPC163693
0.725 Intermediate Similarity NPC147635
0.7232 Intermediate Similarity NPC100078
0.7228 Intermediate Similarity NPC157328
0.7217 Intermediate Similarity NPC475463
0.7207 Intermediate Similarity NPC213528
0.7207 Intermediate Similarity NPC244969
0.7168 Intermediate Similarity NPC306776
0.7117 Intermediate Similarity NPC478181
0.7115 Intermediate Similarity NPC51662
0.7113 Intermediate Similarity NPC179922
0.7103 Intermediate Similarity NPC472237
0.7103 Intermediate Similarity NPC472238
0.7071 Intermediate Similarity NPC475616
0.7037 Intermediate Similarity NPC217567
0.7037 Intermediate Similarity NPC76136
0.7037 Intermediate Similarity NPC329713
0.701 Intermediate Similarity NPC125164
0.701 Intermediate Similarity NPC215030
0.7009 Intermediate Similarity NPC474699
0.7 Intermediate Similarity NPC74466
0.7 Intermediate Similarity NPC470632
0.6975 Remote Similarity NPC470115
0.6975 Remote Similarity NPC470116
0.6939 Remote Similarity NPC228411
0.6923 Remote Similarity NPC478111
0.6893 Remote Similarity NPC474266
0.6881 Remote Similarity NPC470424
0.6864 Remote Similarity NPC473062
0.686 Remote Similarity NPC179429
0.6857 Remote Similarity NPC476717
0.6857 Remote Similarity NPC470657
0.6852 Remote Similarity NPC469627
0.6833 Remote Similarity NPC79193
0.6814 Remote Similarity NPC178853
0.681 Remote Similarity NPC203974
0.6804 Remote Similarity NPC470243
0.6796 Remote Similarity NPC475849
0.6796 Remote Similarity NPC212340
0.6792 Remote Similarity NPC31349
0.6789 Remote Similarity NPC475788
0.6786 Remote Similarity NPC253995
0.6783 Remote Similarity NPC88469
0.6759 Remote Similarity NPC477442
0.6759 Remote Similarity NPC65359
0.6759 Remote Similarity NPC477433
0.6759 Remote Similarity NPC477444
0.6757 Remote Similarity NPC476009
0.6757 Remote Similarity NPC476728
0.6754 Remote Similarity NPC470172
0.6754 Remote Similarity NPC471254
0.675 Remote Similarity NPC97002
0.6729 Remote Similarity NPC53158
0.6727 Remote Similarity NPC206878
0.6719 Remote Similarity NPC188291
0.6699 Remote Similarity NPC216941
0.6698 Remote Similarity NPC92139
0.6697 Remote Similarity NPC474065
0.6696 Remote Similarity NPC471253
0.6696 Remote Similarity NPC261372
0.6696 Remote Similarity NPC473406
0.6696 Remote Similarity NPC263674
0.6696 Remote Similarity NPC58267
0.6695 Remote Similarity NPC236753
0.6695 Remote Similarity NPC228190
0.6694 Remote Similarity NPC317635
0.6694 Remote Similarity NPC475537
0.6694 Remote Similarity NPC329008
0.6694 Remote Similarity NPC308858
0.6667 Remote Similarity NPC474053
0.6667 Remote Similarity NPC477440
0.6667 Remote Similarity NPC287354
0.6667 Remote Similarity NPC477867
0.6667 Remote Similarity NPC477443
0.6667 Remote Similarity NPC304624
0.6667 Remote Similarity NPC475900
0.6667 Remote Similarity NPC62407
0.6639 Remote Similarity NPC277583
0.6636 Remote Similarity NPC475773
0.6636 Remote Similarity NPC239938
0.6635 Remote Similarity NPC102156
0.6635 Remote Similarity NPC148740
0.6634 Remote Similarity NPC474003
0.6612 Remote Similarity NPC209058
0.6607 Remote Similarity NPC116683
0.6607 Remote Similarity NPC475765
0.6607 Remote Similarity NPC193785
0.6607 Remote Similarity NPC475785
0.6581 Remote Similarity NPC252234
0.6577 Remote Similarity NPC309127
0.6577 Remote Similarity NPC247877
0.6574 Remote Similarity NPC471221
0.6566 Remote Similarity NPC474100
0.6566 Remote Similarity NPC473699
0.6566 Remote Similarity NPC473775
0.6566 Remote Similarity NPC475260
0.6566 Remote Similarity NPC51249
0.6566 Remote Similarity NPC475232
0.6565 Remote Similarity NPC100390
0.6565 Remote Similarity NPC254614
0.6555 Remote Similarity NPC469825
0.6555 Remote Similarity NPC475588
0.6552 Remote Similarity NPC473148
0.6549 Remote Similarity NPC472273
0.6549 Remote Similarity NPC323421
0.6549 Remote Similarity NPC328562
0.6549 Remote Similarity NPC474313
0.6545 Remote Similarity NPC216137
0.6529 Remote Similarity NPC473849
0.6529 Remote Similarity NPC312498
0.6522 Remote Similarity NPC298266
0.6522 Remote Similarity NPC259654
0.6522 Remote Similarity NPC67296
0.6518 Remote Similarity NPC215570
0.6514 Remote Similarity NPC200580
0.6512 Remote Similarity NPC2757
0.65 Remote Similarity NPC471884
0.6496 Remote Similarity NPC470167
0.6496 Remote Similarity NPC469629
0.6496 Remote Similarity NPC472756
0.6476 Remote Similarity NPC164289
0.6476 Remote Similarity NPC242771
0.6476 Remote Similarity NPC311642
0.6476 Remote Similarity NPC100366
0.6471 Remote Similarity NPC469826
0.6471 Remote Similarity NPC224414
0.6471 Remote Similarity NPC214030
0.6471 Remote Similarity NPC83108
0.6466 Remote Similarity NPC470117
0.6466 Remote Similarity NPC475376
0.646 Remote Similarity NPC158416
0.646 Remote Similarity NPC470883
0.646 Remote Similarity NPC31645
0.646 Remote Similarity NPC39859
0.646 Remote Similarity NPC76862
0.646 Remote Similarity NPC142529
0.646 Remote Similarity NPC126156
0.646 Remote Similarity NPC91771
0.646 Remote Similarity NPC474297
0.6452 Remote Similarity NPC475238
0.6449 Remote Similarity NPC51267
0.6449 Remote Similarity NPC476715
0.6449 Remote Similarity NPC473350
0.6446 Remote Similarity NPC469824
0.6441 Remote Similarity NPC474101
0.6441 Remote Similarity NPC44004
0.6441 Remote Similarity NPC215408
0.6429 Remote Similarity NPC473331
0.6429 Remote Similarity NPC470423
0.6429 Remote Similarity NPC476849
0.6429 Remote Similarity NPC142882
0.6422 Remote Similarity NPC221993

  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 NPC41674 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
0.8558 High Similarity NPD4057 Clinical (unspecified phase)
0.8558 High Similarity NPD4056 Clinical (unspecified phase)
0.6814 Remote Similarity NPD1700 Approved
0.6356 Remote Similarity NPD8170 Clinical (unspecified phase)
0.626 Remote Similarity NPD7078 Approved
0.6231 Remote Similarity NPD7492 Approved
0.6183 Remote Similarity NPD6616 Approved
0.6172 Remote Similarity NPD6059 Approved
0.6172 Remote Similarity NPD6054 Approved
0.6136 Remote Similarity NPD8293 Discontinued
0.6116 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6095 Remote Similarity NPD4802 Phase 2
0.6095 Remote Similarity NPD4238 Approved
0.609 Remote Similarity NPD7736 Approved
0.6077 Remote Similarity NPD6370 Approved
0.605 Remote Similarity NPD8138 Approved
0.605 Remote Similarity NPD8082 Approved
0.605 Remote Similarity NPD8139 Approved
0.605 Remote Similarity NPD8085 Approved
0.605 Remote Similarity NPD8086 Approved
0.605 Remote Similarity NPD8083 Approved
0.605 Remote Similarity NPD8084 Approved
0.6 Remote Similarity NPD8268 Approved
0.6 Remote Similarity NPD8266 Approved
0.6 Remote Similarity NPD8267 Approved
0.6 Remote Similarity NPD6015 Approved
0.6 Remote Similarity NPD8275 Approved
0.6 Remote Similarity NPD8269 Approved
0.6 Remote Similarity NPD6016 Approved
0.6 Remote Similarity NPD8276 Approved
0.5968 Remote Similarity NPD6371 Approved
0.5954 Remote Similarity NPD5988 Approved
0.595 Remote Similarity NPD8081 Approved
0.5938 Remote Similarity NPD8295 Clinical (unspecified phase)
0.5935 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5923 Remote Similarity NPD6319 Approved
0.5902 Remote Similarity NPD8393 Approved
0.5842 Remote Similarity NPD229 Approved
0.5789 Remote Similarity NPD8328 Phase 3
0.5758 Remote Similarity NPD7909 Approved
0.5748 Remote Similarity NPD6882 Approved
0.5743 Remote Similarity NPD898 Approved
0.5743 Remote Similarity NPD897 Approved
0.5743 Remote Similarity NPD896 Approved
0.5741 Remote Similarity NPD7329 Approved
0.5735 Remote Similarity NPD6033 Approved
0.5693 Remote Similarity NPD7319 Approved
0.5692 Remote Similarity NPD6009 Approved
0.5678 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5656 Remote Similarity NPD8300 Approved
0.5656 Remote Similarity NPD8301 Approved
0.5639 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5635 Remote Similarity NPD6372 Approved
0.5635 Remote Similarity NPD6373 Approved
0.5625 Remote Similarity NPD8297 Approved
0.56 Remote Similarity NPD8140 Approved
0.56 Remote Similarity NPD8307 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