Structure

Physi-Chem Properties

Molecular Weight:  602.27
Volume:  576.559
LogP:  2.979
LogD:  2.242
LogS:  -4.059
# Rotatable Bonds:  2
TPSA:  156.97
# H-Bond Aceptor:  10
# H-Bond Donor:  5
# Rings:  8
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.292
Synthetic Accessibility Score:  6.534
Fsp3:  0.806
Lipinski Rule-of-5:  Accepted
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:  -5.482
MDCK Permeability:  1.057182362274034e-05
Pgp-inhibitor:  0.156
Pgp-substrate:  0.976
Human Intestinal Absorption (HIA):  0.041
20% Bioavailability (F20%):  0.493
30% Bioavailability (F30%):  0.713

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.997
Plasma Protein Binding (PPB):  77.78333282470703%
Volume Distribution (VD):  1.687
Pgp-substrate:  8.938180923461914%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.7
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.297
CYP2C9-inhibitor:  0.041
CYP2C9-substrate:  0.051
CYP2D6-inhibitor:  0.017
CYP2D6-substrate:  0.161
CYP3A4-inhibitor:  0.884
CYP3A4-substrate:  0.835

ADMET: Excretion

Clearance (CL):  3.556
Half-life (T1/2):  0.206

ADMET: Toxicity

hERG Blockers:  0.623
Human Hepatotoxicity (H-HT):  0.212
Drug-inuced Liver Injury (DILI):  0.722
AMES Toxicity:  0.946
Rat Oral Acute Toxicity:  0.967
Maximum Recommended Daily Dose:  0.975
Skin Sensitization:  0.931
Carcinogencity:  0.55
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.973

Download Data

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

  Natural Product: NPC470094

Natural Product ID:  NPC470094
Common Name*:   JHKLDCGHXADNGS-DJHKYUSNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JHKLDCGHXADNGS-DJHKYUSNSA-N
Standard InCHI:  InChI=1S/C31H42N2O8S/c1-16-11-30(33-24(32)14-42-30)31(37)26(39-16)40-22-10-18-3-4-21-20(28(18,15-34)12-23(22)41-31)5-7-27(2)19(6-8-29(21,27)36)17-9-25(35)38-13-17/h9,15-16,18-23,26,36-37H,3-8,10-14H2,1-2H3,(H2,32,33)/t16-,18+,19-,20+,21-,22-,23-,26+,27-,28-,29+,30+,31-/m1/s1
SMILES:  O=C[C@]12C[C@H]3O[C@]4(O)[C@H](O[C@@H]3C[C@@H]1CC[C@@H]1[C@@H]2CC[C@]2([C@]1(O)CC[C@@H]2C1=CC(=O)OC1)C)O[C@@H](C[C@@]14SCC(=N)N1)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL175806
PubChem CID:   44387914
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001125] Steroid lactones
          • [CHEMONTID:0001555] Cardenolides and derivatives
            • [CHEMONTID:0001559] Cardenolide glycosides 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
NPO27807 Calotropis procera Species Apocynaceae Eukaryota root barks n.a. n.a. PMID[15689169]
NPO27807 Calotropis procera Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27807 Calotropis procera Species Apocynaceae 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
NPT933 Cell Line U373 MG Homo sapiens IC50 = 40.0 nM PMID[558335]
NPT148 Cell Line HCT-15 Homo sapiens IC50 = 28.0 nM PMID[558335]
NPT114 Cell Line LoVo Homo sapiens IC50 = 10.0 nM PMID[558335]
NPT81 Cell Line A549 Homo sapiens IC50 = 25.0 nM PMID[558335]
NPT6247 Individual Protein Sodium/potassium-transporting ATPase alpha-1 chain Sus scrofa IC50 = 68.0 nM PMID[558335]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 4.0 nM PMID[558335]
NPT32 Organism Mus musculus Mus musculus MTD = 5.0 mg kg-1 PMID[558335]

☑ 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 NPC470094 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
0.9125 High Similarity NPC473040
0.8589 High Similarity NPC163365
0.8447 Intermediate Similarity NPC473208
0.7452 Intermediate Similarity NPC91
0.7405 Intermediate Similarity NPC16569
0.7405 Intermediate Similarity NPC159338
0.7405 Intermediate Similarity NPC253456
0.7358 Intermediate Similarity NPC19124
0.7358 Intermediate Similarity NPC93416
0.7358 Intermediate Similarity NPC42670
0.7312 Intermediate Similarity NPC477709
0.7312 Intermediate Similarity NPC104585
0.7312 Intermediate Similarity NPC298783
0.7312 Intermediate Similarity NPC225385
0.7312 Intermediate Similarity NPC476221
0.7312 Intermediate Similarity NPC157817
0.7312 Intermediate Similarity NPC142756
0.7233 Intermediate Similarity NPC232785
0.7233 Intermediate Similarity NPC140092
0.7233 Intermediate Similarity NPC329986
0.7233 Intermediate Similarity NPC188234
0.7233 Intermediate Similarity NPC125077
0.7233 Intermediate Similarity NPC276838
0.7222 Intermediate Similarity NPC171619
0.7152 Intermediate Similarity NPC469750
0.7152 Intermediate Similarity NPC250556
0.7107 Intermediate Similarity NPC471356
0.7107 Intermediate Similarity NPC179412
0.7107 Intermediate Similarity NPC240070
0.7107 Intermediate Similarity NPC329784
0.7099 Intermediate Similarity NPC469749
0.7099 Intermediate Similarity NPC32793
0.7099 Intermediate Similarity NPC116075
0.7099 Intermediate Similarity NPC247190
0.7099 Intermediate Similarity NPC146857
0.7099 Intermediate Similarity NPC88668
0.7073 Intermediate Similarity NPC59288
0.7055 Intermediate Similarity NPC329636
0.7025 Intermediate Similarity NPC27363
0.7019 Intermediate Similarity NPC86159
0.7019 Intermediate Similarity NPC70542
0.7019 Intermediate Similarity NPC471358
0.7019 Intermediate Similarity NPC469753
0.7019 Intermediate Similarity NPC17896
0.7019 Intermediate Similarity NPC180079
0.7019 Intermediate Similarity NPC251866
0.7019 Intermediate Similarity NPC469755
0.7019 Intermediate Similarity NPC10823
0.7019 Intermediate Similarity NPC6108
0.7019 Intermediate Similarity NPC89514
0.7019 Intermediate Similarity NPC469754
0.7019 Intermediate Similarity NPC197707
0.7019 Intermediate Similarity NPC471361
0.7019 Intermediate Similarity NPC469752
0.7019 Intermediate Similarity NPC471359
0.7019 Intermediate Similarity NPC219085
0.7019 Intermediate Similarity NPC469751
0.7019 Intermediate Similarity NPC471360
0.7019 Intermediate Similarity NPC9499
0.7019 Intermediate Similarity NPC471352
0.7019 Intermediate Similarity NPC284406
0.7012 Intermediate Similarity NPC194716
0.697 Remote Similarity NPC329675
0.6894 Remote Similarity NPC117702
0.6894 Remote Similarity NPC469757
0.6894 Remote Similarity NPC471357
0.6894 Remote Similarity NPC146456
0.6772 Remote Similarity NPC329905
0.6748 Remote Similarity NPC311534
0.673 Remote Similarity NPC475136
0.673 Remote Similarity NPC474466
0.6688 Remote Similarity NPC196931
0.6667 Remote Similarity NPC292467
0.6667 Remote Similarity NPC61717
0.6667 Remote Similarity NPC289700
0.6667 Remote Similarity NPC244380
0.6667 Remote Similarity NPC470897
0.6667 Remote Similarity NPC265699
0.6667 Remote Similarity NPC469756
0.6667 Remote Similarity NPC62172
0.6667 Remote Similarity NPC55532
0.6667 Remote Similarity NPC236973
0.6667 Remote Similarity NPC32177
0.6667 Remote Similarity NPC30483
0.6646 Remote Similarity NPC152615
0.6629 Remote Similarity NPC113620
0.6629 Remote Similarity NPC187497
0.6629 Remote Similarity NPC100612
0.6629 Remote Similarity NPC174336
0.6629 Remote Similarity NPC475599
0.6627 Remote Similarity NPC155529
0.6627 Remote Similarity NPC471855
0.6625 Remote Similarity NPC72260
0.6625 Remote Similarity NPC475556
0.6625 Remote Similarity NPC470312
0.6625 Remote Similarity NPC475629
0.6604 Remote Similarity NPC218093
0.6588 Remote Similarity NPC290746
0.6588 Remote Similarity NPC75616
0.6588 Remote Similarity NPC79250
0.6584 Remote Similarity NPC231518
0.6584 Remote Similarity NPC173555
0.6584 Remote Similarity NPC120390
0.6584 Remote Similarity NPC474908
0.6584 Remote Similarity NPC314535
0.6584 Remote Similarity NPC40749
0.6584 Remote Similarity NPC475419
0.6584 Remote Similarity NPC475219
0.6584 Remote Similarity NPC475590
0.6582 Remote Similarity NPC193382
0.6582 Remote Similarity NPC138372
0.6582 Remote Similarity NPC106228
0.6582 Remote Similarity NPC99620
0.6582 Remote Similarity NPC310341
0.6582 Remote Similarity NPC199428
0.6582 Remote Similarity NPC5311
0.6573 Remote Similarity NPC475527
0.6568 Remote Similarity NPC477236
0.6568 Remote Similarity NPC127656
0.6566 Remote Similarity NPC173347
0.6562 Remote Similarity NPC9674
0.6562 Remote Similarity NPC19028
0.6562 Remote Similarity NPC81222
0.6562 Remote Similarity NPC291820
0.6552 Remote Similarity NPC214821
0.6552 Remote Similarity NPC298067
0.6545 Remote Similarity NPC477490
0.6545 Remote Similarity NPC114306
0.6543 Remote Similarity NPC74259
0.6543 Remote Similarity NPC264336
0.6543 Remote Similarity NPC28532
0.6543 Remote Similarity NPC193893
0.6543 Remote Similarity NPC474423
0.6541 Remote Similarity NPC77319
0.6541 Remote Similarity NPC471353
0.6541 Remote Similarity NPC27507
0.6541 Remote Similarity NPC158344
0.6541 Remote Similarity NPC244402
0.6541 Remote Similarity NPC471354
0.6541 Remote Similarity NPC99728
0.6541 Remote Similarity NPC142066
0.6541 Remote Similarity NPC50305
0.6541 Remote Similarity NPC196429
0.6541 Remote Similarity NPC243196
0.6541 Remote Similarity NPC84987
0.6541 Remote Similarity NPC87250
0.6541 Remote Similarity NPC309034
0.6541 Remote Similarity NPC473852
0.6541 Remote Similarity NPC471351
0.6541 Remote Similarity NPC471355
0.6541 Remote Similarity NPC157376
0.6541 Remote Similarity NPC34390
0.6541 Remote Similarity NPC474418
0.6541 Remote Similarity NPC93883
0.6522 Remote Similarity NPC107607
0.6519 Remote Similarity NPC84949
0.6519 Remote Similarity NPC69576
0.6519 Remote Similarity NPC471633
0.6519 Remote Similarity NPC31354
0.6509 Remote Similarity NPC158350
0.6506 Remote Similarity NPC471407
0.6503 Remote Similarity NPC117445
0.6503 Remote Similarity NPC308262
0.6503 Remote Similarity NPC208193
0.65 Remote Similarity NPC83287
0.6497 Remote Similarity NPC298005
0.6497 Remote Similarity NPC36463
0.6494 Remote Similarity NPC141669
0.6471 Remote Similarity NPC297058
0.6467 Remote Similarity NPC201359
0.6467 Remote Similarity NPC477493
0.646 Remote Similarity NPC5883
0.646 Remote Similarity NPC29639
0.646 Remote Similarity NPC122971
0.646 Remote Similarity NPC304260
0.646 Remote Similarity NPC477071
0.646 Remote Similarity NPC44899
0.6453 Remote Similarity NPC180770
0.645 Remote Similarity NPC248703
0.645 Remote Similarity NPC477234
0.6446 Remote Similarity NPC473888
0.6438 Remote Similarity NPC290693
0.6438 Remote Similarity NPC203862
0.6429 Remote Similarity NPC477195
0.6429 Remote Similarity NPC478154
0.6424 Remote Similarity NPC47113
0.6424 Remote Similarity NPC174367
0.6416 Remote Similarity NPC172365
0.6416 Remote Similarity NPC82931
0.6416 Remote Similarity NPC210729
0.6407 Remote Similarity NPC476966
0.6407 Remote Similarity NPC231529
0.6402 Remote Similarity NPC41129
0.64 Remote Similarity NPC475892
0.6391 Remote Similarity NPC478151
0.6391 Remote Similarity NPC73829
0.6391 Remote Similarity NPC119794
0.6386 Remote Similarity NPC470780
0.6386 Remote Similarity NPC287423
0.6379 Remote Similarity NPC48414

  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 NPC470094 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
0.8125 Intermediate Similarity NPD7625 Phase 1
0.7152 Intermediate Similarity NPD7507 Approved
0.7019 Intermediate Similarity NPD7319 Approved
0.6625 Remote Similarity NPD8294 Approved
0.6625 Remote Similarity NPD8377 Approved
0.6584 Remote Similarity NPD8296 Approved
0.6584 Remote Similarity NPD8033 Approved
0.6584 Remote Similarity NPD8379 Approved
0.6584 Remote Similarity NPD8335 Approved
0.6584 Remote Similarity NPD8378 Approved
0.6584 Remote Similarity NPD8380 Approved
0.6562 Remote Similarity NPD7516 Approved
0.65 Remote Similarity NPD7328 Approved
0.65 Remote Similarity NPD7327 Approved
0.6205 Remote Similarity NPD6067 Discontinued
0.6154 Remote Similarity NPD7736 Approved
0.6149 Remote Similarity NPD8133 Approved
0.6084 Remote Similarity NPD6291 Clinical (unspecified phase)
0.6084 Remote Similarity NPD7503 Approved
0.6038 Remote Similarity NPD6686 Approved
0.6012 Remote Similarity NPD8449 Approved
0.6012 Remote Similarity NPD8328 Phase 3
0.6 Remote Similarity NPD8293 Discontinued
0.5988 Remote Similarity NPD8390 Approved
0.5988 Remote Similarity NPD8392 Approved
0.5988 Remote Similarity NPD6914 Discontinued
0.5988 Remote Similarity NPD8391 Approved
0.5977 Remote Similarity NPD8450 Suspended
0.5952 Remote Similarity NPD6370 Approved
0.5941 Remote Similarity NPD8451 Approved
0.5932 Remote Similarity NPD6333 Approved
0.5932 Remote Similarity NPD6334 Approved
0.5906 Remote Similarity NPD7078 Approved
0.5906 Remote Similarity NPD8074 Phase 3
0.5906 Remote Similarity NPD8448 Approved
0.5882 Remote Similarity NPD7492 Approved
0.5875 Remote Similarity NPD6412 Phase 2
0.5872 Remote Similarity NPD8337 Approved
0.5872 Remote Similarity NPD8336 Approved
0.5848 Remote Similarity NPD6616 Approved
0.5833 Remote Similarity NPD6059 Approved
0.5833 Remote Similarity NPD6054 Approved
0.5829 Remote Similarity NPD8338 Approved
0.5829 Remote Similarity NPD6845 Suspended
0.5828 Remote Similarity NPD6401 Clinical (unspecified phase)
0.5824 Remote Similarity NPD7122 Discontinued
0.5799 Remote Similarity NPD8513 Phase 3
0.5799 Remote Similarity NPD6908 Approved
0.5799 Remote Similarity NPD8516 Approved
0.5799 Remote Similarity NPD6909 Approved
0.5799 Remote Similarity NPD8517 Approved
0.5799 Remote Similarity NPD8515 Approved
0.5789 Remote Similarity NPD8342 Approved
0.5789 Remote Similarity NPD8340 Approved
0.5789 Remote Similarity NPD8299 Approved
0.5789 Remote Similarity NPD8341 Approved
0.5749 Remote Similarity NPD8295 Clinical (unspecified phase)
0.5749 Remote Similarity NPD6317 Approved
0.5749 Remote Similarity NPD6009 Approved
0.5732 Remote Similarity NPD7638 Approved
0.5731 Remote Similarity NPD7642 Approved
0.5731 Remote Similarity NPD7604 Phase 2
0.5714 Remote Similarity NPD6008 Approved
0.5706 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5706 Remote Similarity NPD6015 Approved
0.5706 Remote Similarity NPD6016 Approved
0.5697 Remote Similarity NPD6882 Approved
0.5696 Remote Similarity NPD7640 Approved
0.5696 Remote Similarity NPD7639 Approved
0.568 Remote Similarity NPD7518 Approved
0.568 Remote Similarity NPD7519 Approved
0.568 Remote Similarity NPD7517 Approved
0.5673 Remote Similarity NPD5988 Approved
0.5663 Remote Similarity NPD4632 Approved
0.5652 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5647 Remote Similarity NPD6319 Approved
0.5642 Remote Similarity NPD8387 Clinical (unspecified phase)
0.564 Remote Similarity NPD7830 Approved
0.564 Remote Similarity NPD7829 Approved
0.5621 Remote Similarity NPD7641 Discontinued
0.5614 Remote Similarity NPD6921 Approved
0.561 Remote Similarity NPD6373 Approved
0.561 Remote Similarity NPD6372 Approved
0.5602 Remote Similarity NPD8297 Approved
0.56 Remote Similarity NPD6033 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