Structure

Physi-Chem Properties

Molecular Weight:  684.52
Volume:  720.729
LogP:  2.547
LogD:  3.632
LogS:  -2.339
# Rotatable Bonds:  20
TPSA:  145.94
# H-Bond Aceptor:  9
# H-Bond Donor:  7
# Rings:  4
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.072
Synthetic Accessibility Score:  5.082
Fsp3:  1.0
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.031
MDCK Permeability:  2.0238221623003483e-06
Pgp-inhibitor:  0.039
Pgp-substrate:  0.959
Human Intestinal Absorption (HIA):  0.943
20% Bioavailability (F20%):  0.477
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.008
Plasma Protein Binding (PPB):  59.36299514770508%
Volume Distribution (VD):  0.505
Pgp-substrate:  36.75921630859375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.027
CYP2C19-inhibitor:  0.006
CYP2C19-substrate:  0.83
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.01
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.516
CYP3A4-inhibitor:  0.055
CYP3A4-substrate:  0.255

ADMET: Excretion

Clearance (CL):  4.342
Half-life (T1/2):  0.035

ADMET: Toxicity

hERG Blockers:  0.548
Human Hepatotoxicity (H-HT):  0.682
Drug-inuced Liver Injury (DILI):  0.051
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.259
Maximum Recommended Daily Dose:  0.271
Skin Sensitization:  0.983
Carcinogencity:  0.007
Eye Corrosion:  0.888
Eye Irritation:  0.014
Respiratory Toxicity:  0.628

Download Data

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

  Natural Product: NPC252564

Natural Product ID:  NPC252564
Common Name*:   Trodusquemine
IUPAC Name:   [(3R,6R)-6-[(3S,5R,7R,8R,9S,10S,13R,14S,17R)-3-[3-[4-(3-aminopropylamino)butylamino]propylamino]-7-hydroxy-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]-2-methylheptan-3-yl] hydrogen sulfate
Synonyms:   MSI-1436; Trodusquemine
Standard InCHIKey:  WUJVPODXELZABP-FWJXURDUSA-N
Standard InCHI:  InChI=1S/C37H72N4O5S/c1-26(2)34(46-47(43,44)45)13-10-27(3)30-11-12-31-35-32(15-17-37(30,31)5)36(4)16-14-29(24-28(36)25-33(35)42)41-23-9-22-40-20-7-6-19-39-21-8-18-38/h26-35,39-42H,6-25,38H2,1-5H3,(H,43,44,45)/t27-,28-,29+,30-,31+,32+,33-,34-,35+,36+,37-/m1/s1
SMILES:  CC(C)[C@@H](CC[C@@H](C)[C@H]1CC[C@H]2[C@H]3[C@H](CC[C@]12C)[C@@]1(C)CC[C@@H](C[C@@H]1C[C@H]3O)NCCCNCCCCNCCCN)OS(=O)(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL508583
PubChem CID:   9917968
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001445] Bile acids, alcohols and derivatives
          • [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives
            • [CHEMONTID:0000260] Monohydroxy bile acids, alcohols and derivatives

*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
NPO26191 Squalus acanthias Species Squalidae Eukaryota n.a. n.a. n.a. PMID[10843574]
NPO40121 Eremophila oppositifolia subsp. Angustifolia Strain Scrophulariaceae Eukaryota n.a. n.a. n.a. PMID[32255628]
NPO40923 Salvia decora Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[32597650]
NPO26191 Squalus acanthias Species Squalidae Eukaryota n.a. n.a. Database[FooDB]
NPO26191 Squalus acanthias Species Squalidae Eukaryota n.a. n.a. Database[FooDB]
NPO26191 Squalus acanthias Species Squalidae 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
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 = 1000.0 nM PMID[552965]
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 = 1300.0 nM PMID[552966]
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 = 1000.0 nM PMID[552967]
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 = 1000.0 nM PMID[552968]
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens Ka = 3.3 10^5/M PMID[552969]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 1.0 ug.mL-1 PMID[552964]
NPT19 Organism Escherichia coli Escherichia coli MIC = 1.0 ug.mL-1 PMID[552964]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 4.0 ug.mL-1 PMID[552964]
NPT20 Organism Candida albicans Candida albicans MIC = 4.0 ug.mL-1 PMID[552964]

☑ 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 NPC252564 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
0.989 High Similarity NPC473537
0.9783 High Similarity NPC475249
0.9677 High Similarity NPC201712
0.9574 High Similarity NPC475518
0.8911 High Similarity NPC473994
0.7857 Intermediate Similarity NPC475340
0.7798 Intermediate Similarity NPC124358
0.7732 Intermediate Similarity NPC21035
0.7474 Intermediate Similarity NPC109533
0.7379 Intermediate Similarity NPC155985
0.7379 Intermediate Similarity NPC174117
0.7027 Intermediate Similarity NPC8009
0.7027 Intermediate Similarity NPC267217
0.7027 Intermediate Similarity NPC83047
0.7027 Intermediate Similarity NPC48127
0.6916 Remote Similarity NPC292819
0.6893 Remote Similarity NPC323156
0.6842 Remote Similarity NPC139778
0.6838 Remote Similarity NPC476955
0.6827 Remote Similarity NPC312637
0.6796 Remote Similarity NPC283751
0.6759 Remote Similarity NPC474164
0.6702 Remote Similarity NPC478103
0.6699 Remote Similarity NPC320478
0.6667 Remote Similarity NPC159390
0.6667 Remote Similarity NPC476903
0.6667 Remote Similarity NPC247891
0.6667 Remote Similarity NPC176012
0.6667 Remote Similarity NPC133995
0.6667 Remote Similarity NPC159367
0.6638 Remote Similarity NPC66862
0.6612 Remote Similarity NPC470593
0.6612 Remote Similarity NPC470594
0.6602 Remote Similarity NPC323958
0.66 Remote Similarity NPC192456
0.6579 Remote Similarity NPC476756
0.6579 Remote Similarity NPC244982
0.6571 Remote Similarity NPC135005
0.6562 Remote Similarity NPC478130
0.6552 Remote Similarity NPC72753
0.6549 Remote Similarity NPC470596
0.6514 Remote Similarity NPC289140
0.6495 Remote Similarity NPC477002
0.6486 Remote Similarity NPC135799
0.6476 Remote Similarity NPC317363
0.6441 Remote Similarity NPC476498
0.6435 Remote Similarity NPC46981
0.6429 Remote Similarity NPC473916
0.6429 Remote Similarity NPC477602
0.6429 Remote Similarity NPC25110
0.6429 Remote Similarity NPC477601
0.6413 Remote Similarity NPC469970
0.6408 Remote Similarity NPC175419
0.6396 Remote Similarity NPC220111
0.6379 Remote Similarity NPC470595
0.6374 Remote Similarity NPC114891
0.6372 Remote Similarity NPC470592
0.6356 Remote Similarity NPC474459
0.6344 Remote Similarity NPC142712
0.6341 Remote Similarity NPC99905
0.6341 Remote Similarity NPC96080
0.6341 Remote Similarity NPC208118
0.6333 Remote Similarity NPC476499
0.6325 Remote Similarity NPC147835
0.6325 Remote Similarity NPC253645
0.6325 Remote Similarity NPC95920
0.6325 Remote Similarity NPC85001
0.6316 Remote Similarity NPC241879
0.6316 Remote Similarity NPC66407
0.6316 Remote Similarity NPC124384
0.6316 Remote Similarity NPC107919
0.6311 Remote Similarity NPC475887
0.6311 Remote Similarity NPC323180
0.6304 Remote Similarity NPC53276
0.6303 Remote Similarity NPC474452
0.6293 Remote Similarity NPC317534
0.6286 Remote Similarity NPC171698
0.6286 Remote Similarity NPC321340
0.6286 Remote Similarity NPC270957
0.6286 Remote Similarity NPC119633
0.6283 Remote Similarity NPC118275
0.6281 Remote Similarity NPC476502
0.6277 Remote Similarity NPC473230
0.6277 Remote Similarity NPC48079
0.6277 Remote Similarity NPC475884
0.6271 Remote Similarity NPC287764
0.6271 Remote Similarity NPC472313
0.6264 Remote Similarity NPC218585
0.6264 Remote Similarity NPC148174
0.6264 Remote Similarity NPC71460
0.625 Remote Similarity NPC232925
0.625 Remote Similarity NPC63588
0.625 Remote Similarity NPC251201
0.625 Remote Similarity NPC192192
0.6237 Remote Similarity NPC477603
0.6237 Remote Similarity NPC41577
0.6237 Remote Similarity NPC473276
0.6237 Remote Similarity NPC474380
0.6218 Remote Similarity NPC79238
0.6211 Remote Similarity NPC472741
0.6211 Remote Similarity NPC271640
0.6207 Remote Similarity NPC55462
0.6207 Remote Similarity NPC477292
0.6204 Remote Similarity NPC84171
0.6186 Remote Similarity NPC252182
0.6186 Remote Similarity NPC470071
0.6186 Remote Similarity NPC109457
0.6186 Remote Similarity NPC100586
0.6186 Remote Similarity NPC187471
0.6186 Remote Similarity NPC157422
0.6186 Remote Similarity NPC1340
0.6186 Remote Similarity NPC127094
0.617 Remote Similarity NPC44122
0.6154 Remote Similarity NPC246956
0.6154 Remote Similarity NPC478053
0.6148 Remote Similarity NPC165396
0.6146 Remote Similarity NPC254037
0.6146 Remote Similarity NPC299948
0.6146 Remote Similarity NPC470830
0.6146 Remote Similarity NPC241085
0.6146 Remote Similarity NPC477820
0.6146 Remote Similarity NPC129829
0.6146 Remote Similarity NPC245223
0.6139 Remote Similarity NPC329117
0.6134 Remote Similarity NPC472359
0.6129 Remote Similarity NPC167995
0.6129 Remote Similarity NPC281540
0.6129 Remote Similarity NPC159654
0.6129 Remote Similarity NPC118937
0.6129 Remote Similarity NPC69149
0.6122 Remote Similarity NPC153719
0.6122 Remote Similarity NPC470610
0.6122 Remote Similarity NPC473238
0.6122 Remote Similarity NPC472341
0.6105 Remote Similarity NPC475172
0.6098 Remote Similarity NPC39485
0.6098 Remote Similarity NPC221196
0.6094 Remote Similarity NPC237286
0.6087 Remote Similarity NPC476755
0.6087 Remote Similarity NPC471083
0.6082 Remote Similarity NPC231945
0.6082 Remote Similarity NPC282454
0.6068 Remote Similarity NPC36497
0.6061 Remote Similarity NPC262050
0.6061 Remote Similarity NPC304499
0.6061 Remote Similarity NPC48795
0.6058 Remote Similarity NPC477599
0.6034 Remote Similarity NPC474583
0.602 Remote Similarity NPC195530
0.602 Remote Similarity NPC473552
0.602 Remote Similarity NPC157777
0.602 Remote Similarity NPC323900
0.602 Remote Similarity NPC477822
0.602 Remote Similarity NPC477821
0.602 Remote Similarity NPC324984
0.602 Remote Similarity NPC473279
0.602 Remote Similarity NPC131506
0.602 Remote Similarity NPC477823
0.6018 Remote Similarity NPC140300
0.6017 Remote Similarity NPC25340
0.6016 Remote Similarity NPC304646
0.6016 Remote Similarity NPC28280
0.6 Remote Similarity NPC158208
0.6 Remote Similarity NPC243027
0.6 Remote Similarity NPC196136
0.6 Remote Similarity NPC476497
0.6 Remote Similarity NPC478054
0.6 Remote Similarity NPC317242
0.5984 Remote Similarity NPC28224
0.5983 Remote Similarity NPC475239
0.5983 Remote Similarity NPC212874
0.5979 Remote Similarity NPC99264
0.5965 Remote Similarity NPC91604
0.596 Remote Similarity NPC232112
0.5954 Remote Similarity NPC476967
0.5948 Remote Similarity NPC50815
0.5943 Remote Similarity NPC320824
0.5941 Remote Similarity NPC163597
0.5941 Remote Similarity NPC4209
0.5938 Remote Similarity NPC63190
0.5934 Remote Similarity NPC476735
0.5923 Remote Similarity NPC476501
0.5922 Remote Similarity NPC220379
0.5918 Remote Similarity NPC473442
0.5918 Remote Similarity NPC120167
0.5906 Remote Similarity NPC476504
0.5902 Remote Similarity NPC56796
0.59 Remote Similarity NPC477508
0.59 Remote Similarity NPC10476
0.59 Remote Similarity NPC192501
0.59 Remote Similarity NPC228994
0.5897 Remote Similarity NPC473254
0.5897 Remote Similarity NPC98765
0.5891 Remote Similarity NPC296686
0.5888 Remote Similarity NPC75810
0.5882 Remote Similarity NPC192046
0.5882 Remote Similarity NPC185915
0.5882 Remote Similarity NPC302578
0.5882 Remote Similarity NPC133596
0.5882 Remote Similarity NPC64081

  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 NPC252564 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
1.0 High Similarity NPD8088 Phase 1
0.989 High Similarity NPD7920 Phase 3
0.989 High Similarity NPD7919 Phase 3
0.7629 Intermediate Similarity NPD8308 Discontinued
0.6944 Remote Similarity NPD8418 Phase 2
0.6726 Remote Similarity NPD7646 Clinical (unspecified phase)
0.6667 Remote Similarity NPD6700 Approved
0.6667 Remote Similarity NPD6701 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8298 Phase 2
0.6604 Remote Similarity NPD6703 Approved
0.6604 Remote Similarity NPD6702 Approved
0.6491 Remote Similarity NPD6920 Discontinued
0.646 Remote Similarity NPD7912 Approved
0.646 Remote Similarity NPD7911 Approved
0.646 Remote Similarity NPD7987 Approved
0.646 Remote Similarity NPD7986 Approved
0.6435 Remote Similarity NPD7990 Approved
0.6435 Remote Similarity NPD7989 Approved
0.6417 Remote Similarity NPD7755 Approved
0.6417 Remote Similarity NPD7754 Approved
0.6348 Remote Similarity NPD8040 Discontinued
0.6316 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6239 Remote Similarity NPD6415 Discontinued
0.6167 Remote Similarity NPD7335 Phase 2
0.6167 Remote Similarity NPD7336 Phase 2
0.6167 Remote Similarity NPD7337 Clinical (unspecified phase)
0.6126 Remote Similarity NPD7991 Discontinued
0.6102 Remote Similarity NPD8174 Phase 2
0.6033 Remote Similarity NPD8077 Approved
0.6033 Remote Similarity NPD8078 Approved
0.5941 Remote Similarity NPD6117 Approved
0.5918 Remote Similarity NPD4787 Phase 1
0.5893 Remote Similarity NPD2636 Clinical (unspecified phase)
0.5893 Remote Similarity NPD2637 Approved
0.5882 Remote Similarity NPD6116 Phase 1
0.5859 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5859 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5825 Remote Similarity NPD6115 Approved
0.5825 Remote Similarity NPD6697 Approved
0.5825 Remote Similarity NPD6114 Approved
0.5825 Remote Similarity NPD6118 Approved
0.5743 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5741 Remote Similarity NPD394 Phase 3
0.5714 Remote Similarity NPD6705 Phase 1
0.5714 Remote Similarity NPD7525 Registered
0.5657 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5657 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5635 Remote Similarity NPD6940 Discontinued
0.5615 Remote Similarity NPD7652 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