Structure

Physi-Chem Properties

Molecular Weight:  558.25
Volume:  536.341
LogP:  2.75
LogD:  1.982
LogS:  -4.762
# Rotatable Bonds:  3
TPSA:  123.66
# H-Bond Aceptor:  10
# H-Bond Donor:  0
# Rings:  8
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.466
Synthetic Accessibility Score:  7.859
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
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:  -5.339
MDCK Permeability:  6.347020098473877e-05
Pgp-inhibitor:  0.994
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.225
30% Bioavailability (F30%):  0.674

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.31
Plasma Protein Binding (PPB):  50.34477996826172%
Volume Distribution (VD):  1.362
Pgp-substrate:  37.856666564941406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.005
CYP1A2-substrate:  0.992
CYP2C19-inhibitor:  0.014
CYP2C19-substrate:  0.72
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.003
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.066
CYP3A4-inhibitor:  0.903
CYP3A4-substrate:  0.643

ADMET: Excretion

Clearance (CL):  14.669
Half-life (T1/2):  0.206

ADMET: Toxicity

hERG Blockers:  0.181
Human Hepatotoxicity (H-HT):  0.739
Drug-inuced Liver Injury (DILI):  0.886
AMES Toxicity:  0.13
Rat Oral Acute Toxicity:  0.972
Maximum Recommended Daily Dose:  0.891
Skin Sensitization:  0.461
Carcinogencity:  0.441
Eye Corrosion:  0.293
Eye Irritation:  0.014
Respiratory Toxicity:  0.989

Download Data

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

  Natural Product: NPC162024

Natural Product ID:  NPC162024
Common Name*:   Rubriflorin A
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WBQRNKRTGAKXNI-DATCFSHWSA-N
Standard InCHI:  InChI=1S/C30H38O10/c1-12-18-21-20(13(2)25(34)36-21)39-30-22(18)27(5,23(12)32)7-8-28(40-30)11-29-15(9-14(37-29)19(28)24(30)33)26(3,4)38-16(29)10-17(31)35-6/h12-16,18-22H,7-11H2,1-6H3/t12-,13-,14+,15-,16+,18+,19-,20+,21+,22-,27-,28-,29+,30-/m0/s1
SMILES:  C[C@H]1[C@@H]2[C@@H]3[C@@H]([C@H](C)C(=O)O3)O[C@]34[C@@H]2[C@](C)(CC[C@@]2(C[C@@]56[C@@H](C[C@H]([C@H]2C3=O)O6)C(C)(C)O[C@@H]5CC(=O)OC)O4)C1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL388392
PubChem CID:   16736657
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001818] Furopyrans

*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
NPT1452 Cell Line C8166 Homo sapiens CC50 = 89.1 ug.mL-1 PMID[527165]
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 EC50 = 10.0 ug.mL-1 PMID[527165]

☑ 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 NPC162024 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 NPC469350
0.91 High Similarity NPC469788
0.91 High Similarity NPC469787
0.91 High Similarity NPC290247
0.8922 High Similarity NPC217041
0.8835 High Similarity NPC182185
0.8812 High Similarity NPC469441
0.8812 High Similarity NPC41674
0.8812 High Similarity NPC228311
0.8667 High Similarity NPC98870
0.8641 High Similarity NPC329876
0.8544 High Similarity NPC176756
0.8462 Intermediate Similarity NPC278693
0.8462 Intermediate Similarity NPC220773
0.8462 Intermediate Similarity NPC167044
0.8269 Intermediate Similarity NPC168890
0.8039 Intermediate Similarity NPC274695
0.8 Intermediate Similarity NPC169089
0.8 Intermediate Similarity NPC114365
0.8 Intermediate Similarity NPC18044
0.8 Intermediate Similarity NPC123070
0.8 Intermediate Similarity NPC88890
0.8 Intermediate Similarity NPC132304
0.8 Intermediate Similarity NPC154962
0.8 Intermediate Similarity NPC177518
0.8 Intermediate Similarity NPC18433
0.781 Intermediate Similarity NPC292803
0.7759 Intermediate Similarity NPC186339
0.7712 Intermediate Similarity NPC11732
0.7652 Intermediate Similarity NPC163693
0.7652 Intermediate Similarity NPC147635
0.7611 Intermediate Similarity NPC475490
0.7596 Intermediate Similarity NPC328180
0.7596 Intermediate Similarity NPC278028
0.7576 Intermediate Similarity NPC314364
0.7521 Intermediate Similarity NPC469351
0.7373 Intermediate Similarity NPC192309
0.7355 Intermediate Similarity NPC172823
0.7339 Intermediate Similarity NPC473526
0.7339 Intermediate Similarity NPC473701
0.7311 Intermediate Similarity NPC1538
0.7311 Intermediate Similarity NPC42747
0.7258 Intermediate Similarity NPC224623
0.7228 Intermediate Similarity NPC51662
0.7156 Intermediate Similarity NPC244969
0.7156 Intermediate Similarity NPC213528
0.7117 Intermediate Similarity NPC306776
0.7117 Intermediate Similarity NPC166079
0.7115 Intermediate Similarity NPC216137
0.7064 Intermediate Similarity NPC478181
0.7048 Intermediate Similarity NPC472237
0.7048 Intermediate Similarity NPC472238
0.7043 Intermediate Similarity NPC471570
0.7027 Intermediate Similarity NPC100078
0.7016 Intermediate Similarity NPC13071
0.699 Remote Similarity NPC221993
0.699 Remote Similarity NPC470009
0.6961 Remote Similarity NPC477441
0.6961 Remote Similarity NPC470657
0.6949 Remote Similarity NPC179429
0.6944 Remote Similarity NPC74466
0.6931 Remote Similarity NPC473791
0.6923 Remote Similarity NPC79193
0.6923 Remote Similarity NPC470116
0.6923 Remote Similarity NPC470115
0.6916 Remote Similarity NPC470191
0.6915 Remote Similarity NPC470243
0.6909 Remote Similarity NPC474053
0.6909 Remote Similarity NPC304624
0.6909 Remote Similarity NPC178853
0.6907 Remote Similarity NPC474003
0.6903 Remote Similarity NPC203974
0.6893 Remote Similarity NPC31349
0.6887 Remote Similarity NPC474379
0.6881 Remote Similarity NPC211087
0.6875 Remote Similarity NPC88469
0.6847 Remote Similarity NPC470172
0.6847 Remote Similarity NPC471254
0.6842 Remote Similarity NPC475275
0.6842 Remote Similarity NPC473771
0.6832 Remote Similarity NPC157328
0.6829 Remote Similarity NPC144625
0.681 Remote Similarity NPC473062
0.6796 Remote Similarity NPC476717
0.6789 Remote Similarity NPC266417
0.6789 Remote Similarity NPC470632
0.6786 Remote Similarity NPC471253
0.6786 Remote Similarity NPC473406
0.6783 Remote Similarity NPC228190
0.6783 Remote Similarity NPC236753
0.6771 Remote Similarity NPC477867
0.6765 Remote Similarity NPC82492
0.6765 Remote Similarity NPC65133
0.6765 Remote Similarity NPC51135
0.6765 Remote Similarity NPC101138
0.6765 Remote Similarity NPC25802
0.6737 Remote Similarity NPC96322
0.6733 Remote Similarity NPC248415
0.6729 Remote Similarity NPC228700
0.6729 Remote Similarity NPC35164
0.6727 Remote Similarity NPC253995
0.6726 Remote Similarity NPC469629
0.6724 Remote Similarity NPC475463
0.67 Remote Similarity NPC1882
0.6698 Remote Similarity NPC477442
0.6698 Remote Similarity NPC477433
0.6698 Remote Similarity NPC477444
0.6697 Remote Similarity NPC476728
0.6697 Remote Similarity NPC145553
0.6697 Remote Similarity NPC193785
0.6667 Remote Similarity NPC188291
0.6667 Remote Similarity NPC476721
0.6639 Remote Similarity NPC308858
0.6639 Remote Similarity NPC475537
0.6638 Remote Similarity NPC469825
0.6635 Remote Similarity NPC469626
0.6635 Remote Similarity NPC243746
0.6635 Remote Similarity NPC475491
0.6607 Remote Similarity NPC471767
0.6606 Remote Similarity NPC287354
0.6606 Remote Similarity NPC62407
0.6604 Remote Similarity NPC200580
0.6604 Remote Similarity NPC477443
0.6604 Remote Similarity NPC477440
0.6598 Remote Similarity NPC215030
0.6587 Remote Similarity NPC2757
0.6579 Remote Similarity NPC470167
0.6569 Remote Similarity NPC102156
0.6569 Remote Similarity NPC148740
0.6555 Remote Similarity NPC97002
0.6552 Remote Similarity NPC469826
0.6549 Remote Similarity NPC49393
0.6549 Remote Similarity NPC105725
0.6549 Remote Similarity NPC250594
0.6545 Remote Similarity NPC475765
0.6538 Remote Similarity NPC478111
0.6538 Remote Similarity NPC51267
0.6538 Remote Similarity NPC470117
0.6531 Remote Similarity NPC179922
0.6525 Remote Similarity NPC469824
0.6522 Remote Similarity NPC215408
0.6522 Remote Similarity NPC291643
0.6514 Remote Similarity NPC470424
0.6514 Remote Similarity NPC309127
0.6514 Remote Similarity NPC217567
0.6514 Remote Similarity NPC247877
0.6514 Remote Similarity NPC76136
0.6514 Remote Similarity NPC329713
0.6514 Remote Similarity NPC206878
0.6512 Remote Similarity NPC100390
0.6512 Remote Similarity NPC254614
0.6509 Remote Similarity NPC471221
0.6505 Remote Similarity NPC474266
0.6504 Remote Similarity NPC329008
0.6504 Remote Similarity NPC317635
0.65 Remote Similarity NPC475616
0.6486 Remote Similarity NPC472273
0.6484 Remote Similarity NPC264192
0.6481 Remote Similarity NPC474699
0.6481 Remote Similarity NPC474065
0.6476 Remote Similarity NPC92139
0.6471 Remote Similarity NPC472230
0.6471 Remote Similarity NPC472229
0.6471 Remote Similarity NPC473849
0.6471 Remote Similarity NPC312498
0.646 Remote Similarity NPC259654
0.646 Remote Similarity NPC298266
0.6455 Remote Similarity NPC305808
0.6455 Remote Similarity NPC215570
0.6446 Remote Similarity NPC277583
0.6442 Remote Similarity NPC115995
0.6441 Remote Similarity NPC470622
0.6435 Remote Similarity NPC244247
0.6429 Remote Similarity NPC470188
0.6429 Remote Similarity NPC125164
0.6422 Remote Similarity NPC161035
0.6415 Remote Similarity NPC239938
0.6412 Remote Similarity NPC475376
0.641 Remote Similarity NPC224414
0.641 Remote Similarity NPC472079
0.641 Remote Similarity NPC475319
0.641 Remote Similarity NPC202898
0.641 Remote Similarity NPC92890
0.6408 Remote Similarity NPC475849
0.6408 Remote Similarity NPC24556
0.6396 Remote Similarity NPC116683
0.6396 Remote Similarity NPC475785
0.6385 Remote Similarity NPC33378
0.6385 Remote Similarity NPC6274
0.6385 Remote Similarity NPC254146
0.6383 Remote Similarity NPC315525
0.6383 Remote Similarity NPC135043
0.6381 Remote Similarity NPC473350
0.6379 Remote Similarity NPC478038
0.6378 Remote Similarity NPC273962
0.6378 Remote Similarity NPC104427
0.6373 Remote Similarity NPC134227
0.6373 Remote Similarity NPC60568
0.6371 Remote Similarity NPC476849
0.6364 Remote Similarity NPC228411

  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 NPC162024 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
0.8 Intermediate Similarity NPD4056 Clinical (unspecified phase)
0.8 Intermediate Similarity NPD4057 Clinical (unspecified phase)
0.6757 Remote Similarity NPD1700 Approved
0.6435 Remote Similarity NPD8170 Clinical (unspecified phase)
0.6404 Remote Similarity NPD8301 Approved
0.6404 Remote Similarity NPD8300 Approved
0.6311 Remote Similarity NPD1779 Approved
0.6311 Remote Similarity NPD1780 Approved
0.6202 Remote Similarity NPD7078 Approved
0.619 Remote Similarity NPD8266 Approved
0.619 Remote Similarity NPD8268 Approved
0.619 Remote Similarity NPD8267 Approved
0.619 Remote Similarity NPD8269 Approved
0.6176 Remote Similarity NPD4238 Approved
0.6176 Remote Similarity NPD4802 Phase 2
0.6172 Remote Similarity NPD7492 Approved
0.6124 Remote Similarity NPD6616 Approved
0.6121 Remote Similarity NPD8085 Approved
0.6121 Remote Similarity NPD8086 Approved
0.6121 Remote Similarity NPD8082 Approved
0.6121 Remote Similarity NPD8083 Approved
0.6121 Remote Similarity NPD8139 Approved
0.6121 Remote Similarity NPD8138 Approved
0.6121 Remote Similarity NPD8084 Approved
0.6111 Remote Similarity NPD6059 Approved
0.6111 Remote Similarity NPD6054 Approved
0.6082 Remote Similarity NPD229 Approved
0.6077 Remote Similarity NPD8293 Discontinued
0.6068 Remote Similarity NPD8275 Approved
0.6068 Remote Similarity NPD8276 Approved
0.6031 Remote Similarity NPD7736 Approved
0.6017 Remote Similarity NPD8081 Approved
0.6016 Remote Similarity NPD6370 Approved
0.6 Remote Similarity NPD8295 Clinical (unspecified phase)
0.5966 Remote Similarity NPD8393 Approved
0.5938 Remote Similarity NPD6015 Approved
0.5938 Remote Similarity NPD6016 Approved
0.5891 Remote Similarity NPD5988 Approved
0.5888 Remote Similarity NPD3670 Clinical (unspecified phase)
0.5888 Remote Similarity NPD3669 Approved
0.5868 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5846 Remote Similarity NPD8328 Phase 3
0.581 Remote Similarity NPD7329 Approved
0.5773 Remote Similarity NPD9496 Clinical (unspecified phase)
0.5736 Remote Similarity NPD6319 Approved
0.5692 Remote Similarity NPD8274 Clinical (unspecified phase)
0.568 Remote Similarity NPD6882 Approved
0.5672 Remote Similarity NPD8337 Approved
0.5672 Remote Similarity NPD8336 Approved
0.5672 Remote Similarity NPD6033 Approved
0.5656 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5656 Remote Similarity NPD8307 Discontinued
0.5656 Remote Similarity NPD8140 Approved
0.5652 Remote Similarity NPD5282 Discontinued
0.5649 Remote Similarity NPD8080 Discontinued
0.5635 Remote Similarity NPD8133 Approved
0.563 Remote Similarity NPD7319 Approved
0.5625 Remote Similarity NPD6009 Approved
0.56 Remote Similarity NPD8413 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