Structure

Physi-Chem Properties

Molecular Weight:  574.21
Volume:  533.989
LogP:  1.758
LogD:  0.795
LogS:  -4.44
# Rotatable Bonds:  0
TPSA:  175.12
# H-Bond Aceptor:  12
# H-Bond Donor:  3
# Rings:  8
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.325
Synthetic Accessibility Score:  7.786
Fsp3:  0.793
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:  -5.367
MDCK Permeability:  2.1698684577131644e-05
Pgp-inhibitor:  0.986
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.593
20% Bioavailability (F20%):  0.997
30% Bioavailability (F30%):  0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.592
Plasma Protein Binding (PPB):  43.79502868652344%
Volume Distribution (VD):  0.933
Pgp-substrate:  40.71055221557617%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.994
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.459
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.001
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.03
CYP3A4-inhibitor:  0.621
CYP3A4-substrate:  0.771

ADMET: Excretion

Clearance (CL):  2.241
Half-life (T1/2):  0.142

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.77
Drug-inuced Liver Injury (DILI):  0.755
AMES Toxicity:  0.981
Rat Oral Acute Toxicity:  0.88
Maximum Recommended Daily Dose:  0.903
Skin Sensitization:  0.796
Carcinogencity:  0.795
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.958

Download Data

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

  Natural Product: NPC469350

Natural Product ID:  NPC469350
Common Name*:   Schirubridilactone D
IUPAC Name:   n.a.
Synonyms:   Schirubridilactone D
Standard InCHIKey:  AXIFZHIVFVUSLT-ZJWCPXNQSA-N
Standard InCHI:  InChI=1S/C29H34O10/c1-11-17-19-18(12(2)22(32)34-19)38-29-20(17)25(5,21(11)31)6-7-26(39-29)10-27-13(8-15-28(26,36-15)23(29)33)24(3,4)35-14(27)9-16(30)37-27/h11-15,17-20H,6-10H2,1-5H3/t11-,12-,13-,14+,15-,17+,18+,19+,20-,25-,26-,27+,28+,29-/m0/s1
SMILES:  CC1C2C3C(C(C(=O)O3)C)OC45C2C(C1=O)(CCC6(O4)CC78C(CC9C6(C5=O)O9)C(OC7CC(=O)O8)(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1076667
PubChem CID:   46182905
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. leaf n.a. PMID[16494492]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. stem n.a. PMID[16494492]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[17190445]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. fruit 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
NPT111 Cell Line K562 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[531388]
NPT65 Cell Line HepG2 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[531388]
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 EC50 = 80.8 ug.mL-1 PMID[531388]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Selectivity Index = 2.2 n.a. PMID[531388]

☑ 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 NPC469350 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
0.9381 High Similarity NPC162024
0.93 High Similarity NPC469788
0.93 High Similarity NPC469787
0.93 High Similarity NPC290247
0.9223 High Similarity NPC98870
0.9208 High Similarity NPC329876
0.9118 High Similarity NPC217041
0.9029 High Similarity NPC182185
0.901 High Similarity NPC228311
0.901 High Similarity NPC469441
0.901 High Similarity NPC41674
0.8738 High Similarity NPC176756
0.8654 High Similarity NPC220773
0.8654 High Similarity NPC167044
0.8654 High Similarity NPC278693
0.8462 Intermediate Similarity NPC168890
0.8416 Intermediate Similarity NPC274695
0.7931 Intermediate Similarity NPC186339
0.785 Intermediate Similarity NPC123070
0.785 Intermediate Similarity NPC88890
0.785 Intermediate Similarity NPC18433
0.785 Intermediate Similarity NPC132304
0.785 Intermediate Similarity NPC169089
0.785 Intermediate Similarity NPC114365
0.785 Intermediate Similarity NPC154962
0.785 Intermediate Similarity NPC177518
0.785 Intermediate Similarity NPC18044
0.7731 Intermediate Similarity NPC11732
0.7672 Intermediate Similarity NPC163693
0.7672 Intermediate Similarity NPC147635
0.7664 Intermediate Similarity NPC292803
0.7542 Intermediate Similarity NPC192309
0.7541 Intermediate Similarity NPC469351
0.7479 Intermediate Similarity NPC1538
0.7453 Intermediate Similarity NPC278028
0.7453 Intermediate Similarity NPC328180
0.7419 Intermediate Similarity NPC224623
0.7377 Intermediate Similarity NPC172823
0.7364 Intermediate Similarity NPC473701
0.7364 Intermediate Similarity NPC473526
0.7333 Intermediate Similarity NPC42747
0.7328 Intermediate Similarity NPC475490
0.7177 Intermediate Similarity NPC13071
0.7103 Intermediate Similarity NPC470191
0.7087 Intermediate Similarity NPC314364
0.7019 Intermediate Similarity NPC470009
0.6992 Remote Similarity NPC144625
0.6949 Remote Similarity NPC470116
0.6949 Remote Similarity NPC470115
0.6947 Remote Similarity NPC470243
0.6947 Remote Similarity NPC96322
0.6937 Remote Similarity NPC474053
0.6937 Remote Similarity NPC304624
0.6916 Remote Similarity NPC474379
0.6875 Remote Similarity NPC244969
0.6875 Remote Similarity NPC213528
0.6842 Remote Similarity NPC306776
0.6842 Remote Similarity NPC166079
0.6827 Remote Similarity NPC469626
0.6827 Remote Similarity NPC475491
0.6822 Remote Similarity NPC216137
0.6818 Remote Similarity NPC266417
0.6796 Remote Similarity NPC473791
0.6786 Remote Similarity NPC478181
0.6786 Remote Similarity NPC471767
0.678 Remote Similarity NPC471570
0.6762 Remote Similarity NPC51662
0.6759 Remote Similarity NPC228700
0.6759 Remote Similarity NPC472237
0.6759 Remote Similarity NPC472238
0.6757 Remote Similarity NPC211087
0.6754 Remote Similarity NPC100078
0.6754 Remote Similarity NPC469629
0.6752 Remote Similarity NPC475463
0.6726 Remote Similarity NPC250594
0.6699 Remote Similarity NPC474266
0.6699 Remote Similarity NPC157328
0.6698 Remote Similarity NPC221993
0.6695 Remote Similarity NPC473062
0.6667 Remote Similarity NPC74466
0.6667 Remote Similarity NPC329008
0.6667 Remote Similarity NPC317635
0.6667 Remote Similarity NPC474699
0.6667 Remote Similarity NPC243746
0.6667 Remote Similarity NPC477441
0.6667 Remote Similarity NPC476717
0.6637 Remote Similarity NPC178853
0.6633 Remote Similarity NPC477867
0.6633 Remote Similarity NPC215030
0.6609 Remote Similarity NPC88469
0.6602 Remote Similarity NPC475849
0.6583 Remote Similarity NPC97002
0.6566 Remote Similarity NPC179922
0.6557 Remote Similarity NPC179429
0.6552 Remote Similarity NPC291643
0.6545 Remote Similarity NPC76136
0.6545 Remote Similarity NPC217567
0.6545 Remote Similarity NPC329713
0.6538 Remote Similarity NPC476721
0.6529 Remote Similarity NPC79193
0.6518 Remote Similarity NPC470632
0.6514 Remote Similarity NPC469627
0.6509 Remote Similarity NPC470657
0.6505 Remote Similarity NPC216941
0.6496 Remote Similarity NPC203974
0.6476 Remote Similarity NPC82492
0.6476 Remote Similarity NPC51135
0.6476 Remote Similarity NPC101138
0.6476 Remote Similarity NPC65133
0.6476 Remote Similarity NPC25802
0.646 Remote Similarity NPC253995
0.6455 Remote Similarity NPC35164
0.6449 Remote Similarity NPC31349
0.6442 Remote Similarity NPC212340
0.6441 Remote Similarity NPC473771
0.6441 Remote Similarity NPC475275
0.6439 Remote Similarity NPC475376
0.6436 Remote Similarity NPC108014
0.6436 Remote Similarity NPC474003
0.6435 Remote Similarity NPC49393
0.6435 Remote Similarity NPC470172
0.6435 Remote Similarity NPC471254
0.6435 Remote Similarity NPC105725
0.6434 Remote Similarity NPC188291
0.6429 Remote Similarity NPC145553
0.6429 Remote Similarity NPC476728
0.6429 Remote Similarity NPC193785
0.6422 Remote Similarity NPC477444
0.6422 Remote Similarity NPC477442
0.6422 Remote Similarity NPC477433
0.6422 Remote Similarity NPC65359
0.6415 Remote Similarity NPC478111
0.6412 Remote Similarity NPC6274
0.6412 Remote Similarity NPC33378
0.6412 Remote Similarity NPC254146
0.6408 Remote Similarity NPC1882
0.64 Remote Similarity NPC142882
0.6396 Remote Similarity NPC477495
0.6396 Remote Similarity NPC470424
0.6391 Remote Similarity NPC219058
0.6391 Remote Similarity NPC256618
0.6387 Remote Similarity NPC227879
0.6387 Remote Similarity NPC208333
0.6387 Remote Similarity NPC228190
0.6387 Remote Similarity NPC236753
0.6379 Remote Similarity NPC471253
0.6379 Remote Similarity NPC473406
0.6379 Remote Similarity NPC34562
0.6373 Remote Similarity NPC475616
0.6372 Remote Similarity NPC263674
0.6372 Remote Similarity NPC261372
0.6372 Remote Similarity NPC58267
0.6364 Remote Similarity NPC474065
0.6355 Remote Similarity NPC474008
0.6341 Remote Similarity NPC277583
0.6339 Remote Similarity NPC167893
0.6339 Remote Similarity NPC287354
0.6339 Remote Similarity NPC62407
0.633 Remote Similarity NPC200580
0.633 Remote Similarity NPC477440
0.633 Remote Similarity NPC477443
0.6316 Remote Similarity NPC470117
0.6316 Remote Similarity NPC157518
0.6316 Remote Similarity NPC470188
0.63 Remote Similarity NPC125164
0.629 Remote Similarity NPC471146
0.6288 Remote Similarity NPC100390
0.6288 Remote Similarity NPC254614
0.6286 Remote Similarity NPC248415
0.6286 Remote Similarity NPC148740
0.6286 Remote Similarity NPC102156
0.6283 Remote Similarity NPC475765
0.6281 Remote Similarity NPC475495
0.6271 Remote Similarity NPC474101
0.6271 Remote Similarity NPC252234
0.626 Remote Similarity NPC264192
0.626 Remote Similarity NPC308858
0.626 Remote Similarity NPC475537
0.625 Remote Similarity NPC309127
0.625 Remote Similarity NPC247877
0.625 Remote Similarity NPC206878
0.625 Remote Similarity NPC135043
0.625 Remote Similarity NPC315525
0.625 Remote Similarity NPC469825
0.6239 Remote Similarity NPC477614
0.6239 Remote Similarity NPC226491
0.6239 Remote Similarity NPC191221
0.6239 Remote Similarity NPC53158
0.6239 Remote Similarity NPC471221
0.6239 Remote Similarity NPC473148
0.6238 Remote Similarity NPC228411
0.6231 Remote Similarity NPC2757
0.623 Remote Similarity NPC473522
0.623 Remote Similarity NPC477093
0.623 Remote Similarity NPC477489
0.623 Remote Similarity NPC475277
0.6228 Remote Similarity NPC472273
0.6226 Remote Similarity NPC472847
0.6216 Remote Similarity NPC191339
0.6216 Remote Similarity NPC286341

  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 NPC469350 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
0.785 Intermediate Similarity NPD4057 Clinical (unspecified phase)
0.785 Intermediate Similarity NPD4056 Clinical (unspecified phase)
0.6937 Remote Similarity NPD1700 Approved
0.6293 Remote Similarity NPD8301 Approved
0.6293 Remote Similarity NPD8300 Approved
0.6058 Remote Similarity NPD4238 Approved
0.6058 Remote Similarity NPD4802 Phase 2
0.605 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5985 Remote Similarity NPD7078 Approved
0.596 Remote Similarity NPD229 Approved
0.5954 Remote Similarity NPD7492 Approved
0.5909 Remote Similarity NPD6616 Approved
0.5891 Remote Similarity NPD6059 Approved
0.5891 Remote Similarity NPD6054 Approved
0.5888 Remote Similarity NPD1780 Approved
0.5888 Remote Similarity NPD1779 Approved
0.5865 Remote Similarity NPD8293 Discontinued
0.5846 Remote Similarity NPD8268 Approved
0.5846 Remote Similarity NPD8266 Approved
0.5846 Remote Similarity NPD8267 Approved
0.5846 Remote Similarity NPD8269 Approved
0.5821 Remote Similarity NPD7736 Approved
0.5802 Remote Similarity NPD6370 Approved
0.575 Remote Similarity NPD8085 Approved
0.575 Remote Similarity NPD8138 Approved
0.575 Remote Similarity NPD8082 Approved
0.575 Remote Similarity NPD8083 Approved
0.575 Remote Similarity NPD8084 Approved
0.575 Remote Similarity NPD8086 Approved
0.575 Remote Similarity NPD8139 Approved
0.5725 Remote Similarity NPD6016 Approved
0.5725 Remote Similarity NPD6015 Approved
0.5702 Remote Similarity NPD8276 Approved
0.5702 Remote Similarity NPD8275 Approved
0.5691 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5682 Remote Similarity NPD5988 Approved
0.5659 Remote Similarity NPD8295 Clinical (unspecified phase)
0.5657 Remote Similarity NPD9496 Clinical (unspecified phase)
0.5656 Remote Similarity NPD8081 Approved
0.5645 Remote Similarity NPD5345 Clinical (unspecified phase)
0.561 Remote Similarity NPD6008 Approved
0.561 Remote Similarity NPD8393 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