Structure

Physi-Chem Properties

Molecular Weight:  558.21
Volume:  519.279
LogP:  1.576
LogD:  0.625
LogS:  -4.439
# Rotatable Bonds:  1
TPSA:  147.19
# H-Bond Aceptor:  11
# H-Bond Donor:  1
# Rings:  9
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.363
Synthetic Accessibility Score:  4.716
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:  -5.377
MDCK Permeability:  4.429757609614171e-05
Pgp-inhibitor:  0.961
Pgp-substrate:  0.066
Human Intestinal Absorption (HIA):  0.03
20% Bioavailability (F20%):  0.988
30% Bioavailability (F30%):  0.906

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.857
Plasma Protein Binding (PPB):  57.093780517578125%
Volume Distribution (VD):  0.632
Pgp-substrate:  46.79512023925781%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.994
CYP2C19-inhibitor:  0.011
CYP2C19-substrate:  0.563
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.002
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.042
CYP3A4-inhibitor:  0.945
CYP3A4-substrate:  0.892

ADMET: Excretion

Clearance (CL):  12.392
Half-life (T1/2):  0.346

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.245
Drug-inuced Liver Injury (DILI):  0.892
AMES Toxicity:  0.982
Rat Oral Acute Toxicity:  0.987
Maximum Recommended Daily Dose:  0.947
Skin Sensitization:  0.894
Carcinogencity:  0.91
Eye Corrosion:  0.116
Eye Irritation:  0.015
Respiratory Toxicity:  0.986

Download Data

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

  Natural Product: NPC329876

Natural Product ID:  NPC329876
Common Name*:   Schigrandilactone B
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BUPVNIVIQIJHNI-HOVTYTAYSA-N
Standard InCHI:  InChI=1S/C29H34O11/c1-12-9-27(38-21(12)33)18-13(2)20(32)23(3)5-6-25-10-26-14(24(4,11-30)35-15(26)8-17(31)37-26)7-16-28(25,36-16)22(34)29(39-25,40-27)19(18)23/h12-16,18-19,30H,5-11H2,1-4H3/t12-,13-,14-,15+,16-,18-,19-,23-,24-,25-,26+,27-,28+,29+/m0/s1
SMILES:  CC1CC2(C3C(C(=O)C4(C3C5(O2)C(=O)C67C(O6)CC8C(OC9C8(CC7(O5)CC4)OC(=O)C9)(C)CO)C)C)OC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1078812
PubChem CID:   44482063
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
NPO19011 Schisandra grandiflora Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[19685905]
NPO19011 Schisandra grandiflora 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
NPT111 Cell Line K562 Homo sapiens IC50 = 3.19 ug.mL-1 PMID[547081]
NPT65 Cell Line HepG2 Homo sapiens IC50 = 0.2 ug.mL-1 PMID[547081]
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 EC50 = 20.8 ug.mL-1 PMID[547081]
NPT2 Others Unspecified Ratio CC50/EC50 = 4.0 n.a. PMID[547081]

☑ 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 NPC329876 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
0.9798 High Similarity NPC469441
0.9798 High Similarity NPC41674
0.9798 High Similarity NPC228311
0.9505 High Similarity NPC290247
0.9505 High Similarity NPC469787
0.9505 High Similarity NPC469788
0.9423 High Similarity NPC98870
0.9412 High Similarity NPC220773
0.9412 High Similarity NPC278693
0.932 High Similarity NPC217041
0.9231 High Similarity NPC182185
0.9216 High Similarity NPC168890
0.9208 High Similarity NPC469350
0.9 High Similarity NPC274695
0.8942 High Similarity NPC176756
0.8857 High Similarity NPC167044
0.8641 High Similarity NPC162024
0.8396 Intermediate Similarity NPC169089
0.8396 Intermediate Similarity NPC18433
0.8396 Intermediate Similarity NPC123070
0.8396 Intermediate Similarity NPC18044
0.8396 Intermediate Similarity NPC132304
0.8396 Intermediate Similarity NPC177518
0.8396 Intermediate Similarity NPC154962
0.8396 Intermediate Similarity NPC88890
0.8396 Intermediate Similarity NPC114365
0.8208 Intermediate Similarity NPC292803
0.8 Intermediate Similarity NPC278028
0.8 Intermediate Similarity NPC328180
0.7966 Intermediate Similarity NPC186339
0.7815 Intermediate Similarity NPC1538
0.7769 Intermediate Similarity NPC11732
0.7742 Intermediate Similarity NPC224623
0.7731 Intermediate Similarity NPC192309
0.7642 Intermediate Similarity NPC13071
0.7581 Intermediate Similarity NPC469351
0.7568 Intermediate Similarity NPC473526
0.7568 Intermediate Similarity NPC473701
0.7561 Intermediate Similarity NPC172823
0.7521 Intermediate Similarity NPC42747
0.7477 Intermediate Similarity NPC470191
0.7459 Intermediate Similarity NPC144625
0.7373 Intermediate Similarity NPC475490
0.7353 Intermediate Similarity NPC473791
0.7308 Intermediate Similarity NPC314364
0.7273 Intermediate Similarity NPC211087
0.7238 Intermediate Similarity NPC470009
0.7196 Intermediate Similarity NPC474699
0.7193 Intermediate Similarity NPC166079
0.7143 Intermediate Similarity NPC470115
0.7143 Intermediate Similarity NPC470116
0.7131 Intermediate Similarity NPC147635
0.7131 Intermediate Similarity NPC163693
0.7105 Intermediate Similarity NPC100078
0.7094 Intermediate Similarity NPC475463
0.7087 Intermediate Similarity NPC157328
0.708 Intermediate Similarity NPC213528
0.708 Intermediate Similarity NPC244969
0.7043 Intermediate Similarity NPC306776
0.7037 Intermediate Similarity NPC469627
0.6991 Remote Similarity NPC478181
0.699 Remote Similarity NPC212340
0.6981 Remote Similarity NPC51662
0.6972 Remote Similarity NPC472237
0.6972 Remote Similarity NPC472238
0.697 Remote Similarity NPC179922
0.6944 Remote Similarity NPC65359
0.6931 Remote Similarity NPC475616
0.6923 Remote Similarity NPC474266
0.6917 Remote Similarity NPC97002
0.6909 Remote Similarity NPC76136
0.6909 Remote Similarity NPC329713
0.6909 Remote Similarity NPC217567
0.6891 Remote Similarity NPC473062
0.6875 Remote Similarity NPC470632
0.6875 Remote Similarity NPC74466
0.6869 Remote Similarity NPC125164
0.6869 Remote Similarity NPC215030
0.6855 Remote Similarity NPC329008
0.6855 Remote Similarity NPC317635
0.6827 Remote Similarity NPC475849
0.68 Remote Similarity NPC228411
0.6792 Remote Similarity NPC478111
0.6757 Remote Similarity NPC470424
0.6748 Remote Similarity NPC179429
0.6731 Remote Similarity NPC216941
0.6729 Remote Similarity NPC476717
0.6729 Remote Similarity NPC470657
0.6721 Remote Similarity NPC79193
0.6696 Remote Similarity NPC178853
0.6695 Remote Similarity NPC203974
0.6667 Remote Similarity NPC88469
0.6667 Remote Similarity NPC475788
0.6667 Remote Similarity NPC31349
0.6667 Remote Similarity NPC253995
0.6667 Remote Similarity NPC470243
0.6638 Remote Similarity NPC471254
0.6638 Remote Similarity NPC470172
0.6637 Remote Similarity NPC476009
0.6637 Remote Similarity NPC476728
0.6636 Remote Similarity NPC477442
0.6636 Remote Similarity NPC477444
0.6636 Remote Similarity NPC477433
0.6617 Remote Similarity NPC475376
0.6615 Remote Similarity NPC188291
0.661 Remote Similarity NPC44004
0.661 Remote Similarity NPC474101
0.6607 Remote Similarity NPC206878
0.6606 Remote Similarity NPC53158
0.6602 Remote Similarity NPC470014
0.6587 Remote Similarity NPC142882
0.6585 Remote Similarity NPC308858
0.6585 Remote Similarity NPC475537
0.6583 Remote Similarity NPC236753
0.6583 Remote Similarity NPC228190
0.6583 Remote Similarity NPC227879
0.6583 Remote Similarity NPC208333
0.6581 Remote Similarity NPC473406
0.6581 Remote Similarity NPC34562
0.6581 Remote Similarity NPC471253
0.6579 Remote Similarity NPC261372
0.6579 Remote Similarity NPC58267
0.6579 Remote Similarity NPC263674
0.6577 Remote Similarity NPC474065
0.6574 Remote Similarity NPC469626
0.6574 Remote Similarity NPC475491
0.6574 Remote Similarity NPC92139
0.6567 Remote Similarity NPC256618
0.6567 Remote Similarity NPC219058
0.6552 Remote Similarity NPC304624
0.6552 Remote Similarity NPC474053
0.6552 Remote Similarity NPC471767
0.6549 Remote Similarity NPC287354
0.6549 Remote Similarity NPC17336
0.6549 Remote Similarity NPC62407
0.6549 Remote Similarity NPC475900
0.6545 Remote Similarity NPC477443
0.6545 Remote Similarity NPC477440
0.6535 Remote Similarity NPC477867
0.6532 Remote Similarity NPC277583
0.6514 Remote Similarity NPC239938
0.6514 Remote Similarity NPC475773
0.6509 Remote Similarity NPC148740
0.6509 Remote Similarity NPC102156
0.6505 Remote Similarity NPC474003
0.6504 Remote Similarity NPC209058
0.65 Remote Similarity NPC117604
0.6496 Remote Similarity NPC250594
0.6491 Remote Similarity NPC475765
0.6491 Remote Similarity NPC193785
0.6491 Remote Similarity NPC475785
0.6491 Remote Similarity NPC116683
0.648 Remote Similarity NPC471146
0.6471 Remote Similarity NPC252234
0.6466 Remote Similarity NPC100390
0.6466 Remote Similarity NPC33378
0.6466 Remote Similarity NPC254146
0.6466 Remote Similarity NPC254614
0.6466 Remote Similarity NPC6274
0.646 Remote Similarity NPC470423
0.646 Remote Similarity NPC247877
0.646 Remote Similarity NPC309127
0.6455 Remote Similarity NPC477614
0.6455 Remote Similarity NPC226491
0.6455 Remote Similarity NPC471221
0.6446 Remote Similarity NPC469825
0.6446 Remote Similarity NPC475588
0.6441 Remote Similarity NPC473148
0.6436 Remote Similarity NPC473699
0.6436 Remote Similarity NPC475260
0.6436 Remote Similarity NPC51249
0.6436 Remote Similarity NPC475232
0.6436 Remote Similarity NPC473775
0.6436 Remote Similarity NPC474100
0.6435 Remote Similarity NPC328562
0.6435 Remote Similarity NPC474313
0.6435 Remote Similarity NPC323421
0.6435 Remote Similarity NPC472273
0.6429 Remote Similarity NPC216137
0.6429 Remote Similarity NPC475401
0.6423 Remote Similarity NPC477489
0.6423 Remote Similarity NPC312498
0.6423 Remote Similarity NPC473849
0.6422 Remote Similarity NPC472745
0.6412 Remote Similarity NPC2757
0.641 Remote Similarity NPC67296
0.641 Remote Similarity NPC259654
0.641 Remote Similarity NPC298266
0.6404 Remote Similarity NPC215570
0.6396 Remote Similarity NPC200580
0.6393 Remote Similarity NPC471884
0.6391 Remote Similarity NPC475389
0.6391 Remote Similarity NPC473838
0.6387 Remote Similarity NPC472756
0.6387 Remote Similarity NPC469629
0.6387 Remote Similarity NPC470167
0.6379 Remote Similarity NPC476294
0.6378 Remote Similarity NPC477092
0.6372 Remote Similarity NPC474379
0.6372 Remote Similarity NPC475488

  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 NPC329876 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
0.8396 Intermediate Similarity NPD4057 Clinical (unspecified phase)
0.8396 Intermediate Similarity NPD4056 Clinical (unspecified phase)
0.6991 Remote Similarity NPD1700 Approved
0.625 Remote Similarity NPD8170 Clinical (unspecified phase)
0.6165 Remote Similarity NPD7078 Approved
0.6136 Remote Similarity NPD7492 Approved
0.609 Remote Similarity NPD6616 Approved
0.6077 Remote Similarity NPD6059 Approved
0.6077 Remote Similarity NPD6054 Approved
0.6045 Remote Similarity NPD8293 Discontinued
0.6016 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6 Remote Similarity NPD6371 Approved
0.6 Remote Similarity NPD7736 Approved
0.5985 Remote Similarity NPD6370 Approved
0.5981 Remote Similarity NPD4238 Approved
0.5981 Remote Similarity NPD4802 Phase 2
0.595 Remote Similarity NPD8139 Approved
0.595 Remote Similarity NPD8085 Approved
0.595 Remote Similarity NPD8083 Approved
0.595 Remote Similarity NPD8138 Approved
0.595 Remote Similarity NPD8084 Approved
0.595 Remote Similarity NPD8082 Approved
0.595 Remote Similarity NPD8086 Approved
0.5909 Remote Similarity NPD8266 Approved
0.5909 Remote Similarity NPD8268 Approved
0.5909 Remote Similarity NPD6015 Approved
0.5909 Remote Similarity NPD8269 Approved
0.5909 Remote Similarity NPD8267 Approved
0.5909 Remote Similarity NPD6016 Approved
0.5902 Remote Similarity NPD8275 Approved
0.5902 Remote Similarity NPD8276 Approved
0.5865 Remote Similarity NPD5988 Approved
0.5854 Remote Similarity NPD8081 Approved
0.5846 Remote Similarity NPD8295 Clinical (unspecified phase)
0.584 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6319 Approved
0.582 Remote Similarity NPD8301 Approved
0.582 Remote Similarity NPD8300 Approved
0.5806 Remote Similarity NPD8393 Approved
0.5728 Remote Similarity NPD229 Approved
0.5704 Remote Similarity NPD8328 Phase 3
0.5659 Remote Similarity NPD6882 Approved
0.5652 Remote Similarity NPD6033 Approved
0.5644 Remote Similarity NPD7909 Approved
0.5636 Remote Similarity NPD7329 Approved
0.5631 Remote Similarity NPD896 Approved
0.5631 Remote Similarity NPD898 Approved
0.5631 Remote Similarity NPD897 Approved
0.5612 Remote Similarity NPD7319 Approved
0.5606 Remote Similarity NPD6009 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