Structure

Physi-Chem Properties

Molecular Weight:  424.35
Volume:  478.856
LogP:  4.84
LogD:  3.918
LogS:  -5.318
# Rotatable Bonds:  5
TPSA:  32.34
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.451
Synthetic Accessibility Score:  4.904
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.608
MDCK Permeability:  9.443084309168626e-06
Pgp-inhibitor:  0.998
Pgp-substrate:  0.051
Human Intestinal Absorption (HIA):  0.022
20% Bioavailability (F20%):  0.96
30% Bioavailability (F30%):  0.374

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.222
Plasma Protein Binding (PPB):  85.41161346435547%
Volume Distribution (VD):  1.294
Pgp-substrate:  5.099246025085449%

ADMET: Metabolism

CYP1A2-inhibitor:  0.053
CYP1A2-substrate:  0.917
CYP2C19-inhibitor:  0.333
CYP2C19-substrate:  0.961
CYP2C9-inhibitor:  0.426
CYP2C9-substrate:  0.078
CYP2D6-inhibitor:  0.933
CYP2D6-substrate:  0.921
CYP3A4-inhibitor:  0.941
CYP3A4-substrate:  0.824

ADMET: Excretion

Clearance (CL):  5.217
Half-life (T1/2):  0.138

ADMET: Toxicity

hERG Blockers:  0.107
Human Hepatotoxicity (H-HT):  0.345
Drug-inuced Liver Injury (DILI):  0.227
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.889
Maximum Recommended Daily Dose:  0.906
Skin Sensitization:  0.346
Carcinogencity:  0.692
Eye Corrosion:  0.003
Eye Irritation:  0.013
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC166458

Natural Product ID:  NPC166458
Common Name*:   (E)-N-[(3S,8R,9S,10R,13R,17S)-17-[(1S)-1-(Dimethylamino)Ethyl]-10,13-Dimethyl-2,3,6,7,8,9,11,12,16,17-Decahydro-1H-Cyclopenta[A]Phenanthren-3-Yl]-2-Methylbut-2-Enamide
IUPAC Name:   (E)-N-[(3S,8R,9S,10R,13R,17S)-17-[(1S)-1-(dimethylamino)ethyl]-10,13-dimethyl-2,3,6,7,8,9,11,12,16,17-decahydro-1H-cyclopenta[a]phenanthren-3-yl]-2-methylbut-2-enamide
Synonyms:  
Standard InCHIKey:  WKBYYEDQGZSMCP-CNLUTGEBSA-N
Standard InCHI:  InChI=1S/C28H44N2O/c1-8-18(2)26(31)29-21-13-15-27(4)20(17-21)9-10-22-24-12-11-23(19(3)30(6)7)28(24,5)16-14-25(22)27/h8,12,17,19,21-23,25H,9-11,13-16H2,1-7H3,(H,29,31)/b18-8+/t19-,21-,22-,23+,25-,27-,28+/m0/s1
SMILES:  C/C=C(/C(=N[C@H]1CC[C@]2(C(=C1)CC[C@@H]1[C@@H]2CC[C@]2(C1=CC[C@@H]2[C@@H](N(C)C)C)C)C)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL136251
PubChem CID:   11373632
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002340] Azasteroids 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
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[14584959]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[14643329]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[9548847]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27888 Sarcococca saligna Species Buxaceae 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
NPT204 Individual Protein Acetylcholinesterase Homo sapiens IC50 = 7762.47 nM PMID[480182]

☑ 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 NPC166458 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
0.8706 High Similarity NPC152684
0.8511 High Similarity NPC247060
0.8316 Intermediate Similarity NPC226509
0.8316 Intermediate Similarity NPC50815
0.825 Intermediate Similarity NPC265789
0.8235 Intermediate Similarity NPC257962
0.8125 Intermediate Similarity NPC471083
0.8125 Intermediate Similarity NPC152718
0.7959 Intermediate Similarity NPC469958
0.7879 Intermediate Similarity NPC55462
0.7805 Intermediate Similarity NPC21773
0.7727 Intermediate Similarity NPC224072
0.7708 Intermediate Similarity NPC167419
0.7677 Intermediate Similarity NPC90538
0.7619 Intermediate Similarity NPC476904
0.7573 Intermediate Similarity NPC472359
0.7528 Intermediate Similarity NPC39966
0.7528 Intermediate Similarity NPC215474
0.7442 Intermediate Similarity NPC7214
0.7391 Intermediate Similarity NPC157479
0.7386 Intermediate Similarity NPC211322
0.7353 Intermediate Similarity NPC230677
0.7308 Intermediate Similarity NPC175585
0.7283 Intermediate Similarity NPC24733
0.7282 Intermediate Similarity NPC25340
0.7273 Intermediate Similarity NPC140685
0.7264 Intermediate Similarity NPC469968
0.7264 Intermediate Similarity NPC80834
0.7234 Intermediate Similarity NPC34754
0.72 Intermediate Similarity NPC275686
0.7172 Intermediate Similarity NPC140300
0.7143 Intermediate Similarity NPC283277
0.7126 Intermediate Similarity NPC125828
0.7097 Intermediate Similarity NPC147513
0.7097 Intermediate Similarity NPC75810
0.7071 Intermediate Similarity NPC476903
0.7065 Intermediate Similarity NPC171639
0.7041 Intermediate Similarity NPC243985
0.7041 Intermediate Similarity NPC280710
0.7033 Intermediate Similarity NPC118329
0.7033 Intermediate Similarity NPC474122
0.7033 Intermediate Similarity NPC152039
0.6991 Remote Similarity NPC472458
0.699 Remote Similarity NPC474583
0.699 Remote Similarity NPC293299
0.699 Remote Similarity NPC45365
0.6957 Remote Similarity NPC472312
0.6944 Remote Similarity NPC56796
0.6941 Remote Similarity NPC245223
0.6939 Remote Similarity NPC93027
0.6923 Remote Similarity NPC12035
0.6907 Remote Similarity NPC84171
0.6903 Remote Similarity NPC242692
0.69 Remote Similarity NPC247220
0.6863 Remote Similarity NPC135799
0.6854 Remote Similarity NPC476308
0.6848 Remote Similarity NPC329782
0.6832 Remote Similarity NPC240650
0.6832 Remote Similarity NPC184033
0.6804 Remote Similarity NPC249312
0.68 Remote Similarity NPC311164
0.68 Remote Similarity NPC272732
0.6765 Remote Similarity NPC91604
0.6744 Remote Similarity NPC472831
0.6701 Remote Similarity NPC324405
0.6667 Remote Similarity NPC90150
0.6667 Remote Similarity NPC474164
0.6667 Remote Similarity NPC237286
0.6667 Remote Similarity NPC4834
0.6591 Remote Similarity NPC476329
0.6588 Remote Similarity NPC37792
0.6581 Remote Similarity NPC109151
0.6574 Remote Similarity NPC159367
0.6562 Remote Similarity NPC311769
0.6562 Remote Similarity NPC182106
0.6552 Remote Similarity NPC138409
0.6552 Remote Similarity NPC124384
0.6542 Remote Similarity NPC36497
0.6526 Remote Similarity NPC21667
0.6517 Remote Similarity NPC474743
0.6509 Remote Similarity NPC241879
0.6506 Remote Similarity NPC219621
0.6484 Remote Similarity NPC244488
0.6484 Remote Similarity NPC247325
0.6476 Remote Similarity NPC118275
0.6429 Remote Similarity NPC43308
0.6415 Remote Similarity NPC58200
0.6415 Remote Similarity NPC176012
0.6408 Remote Similarity NPC289140
0.6396 Remote Similarity NPC66862
0.6364 Remote Similarity NPC259252
0.633 Remote Similarity NPC46981
0.633 Remote Similarity NPC169375
0.6327 Remote Similarity NPC56107
0.6316 Remote Similarity NPC475724
0.6316 Remote Similarity NPC165396
0.6306 Remote Similarity NPC328052
0.6296 Remote Similarity NPC119329
0.6296 Remote Similarity NPC212874
0.6292 Remote Similarity NPC475728
0.6277 Remote Similarity NPC30986
0.6277 Remote Similarity NPC109546
0.6277 Remote Similarity NPC28862
0.6277 Remote Similarity NPC143182
0.6277 Remote Similarity NPC209430
0.6277 Remote Similarity NPC47982
0.6277 Remote Similarity NPC81306
0.6277 Remote Similarity NPC84694
0.625 Remote Similarity NPC472867
0.6214 Remote Similarity NPC476754
0.6214 Remote Similarity NPC477290
0.6211 Remote Similarity NPC234193
0.6204 Remote Similarity NPC474563
0.619 Remote Similarity NPC3202
0.619 Remote Similarity NPC311809
0.618 Remote Similarity NPC184919
0.617 Remote Similarity NPC474216
0.6168 Remote Similarity NPC77703
0.6163 Remote Similarity NPC476682
0.6161 Remote Similarity NPC72753
0.6146 Remote Similarity NPC209620
0.6146 Remote Similarity NPC23852
0.6146 Remote Similarity NPC264245
0.6136 Remote Similarity NPC476135
0.6118 Remote Similarity NPC469728
0.6118 Remote Similarity NPC29468
0.6091 Remote Similarity NPC86906
0.6091 Remote Similarity NPC477292
0.6082 Remote Similarity NPC101462
0.6082 Remote Similarity NPC189972
0.6082 Remote Similarity NPC49964
0.6082 Remote Similarity NPC50964
0.6082 Remote Similarity NPC472239
0.6071 Remote Similarity NPC21781
0.6071 Remote Similarity NPC472827
0.6071 Remote Similarity NPC309825
0.6067 Remote Similarity NPC160209
0.6064 Remote Similarity NPC91665
0.6058 Remote Similarity NPC473314
0.6055 Remote Similarity NPC473254
0.6042 Remote Similarity NPC476560
0.6042 Remote Similarity NPC209944
0.6042 Remote Similarity NPC164840
0.6042 Remote Similarity NPC241290
0.604 Remote Similarity NPC316186
0.6024 Remote Similarity NPC11130
0.6023 Remote Similarity NPC242945
0.6023 Remote Similarity NPC222366
0.6023 Remote Similarity NPC259156
0.6023 Remote Similarity NPC286669
0.6023 Remote Similarity NPC476039
0.6023 Remote Similarity NPC279434
0.6022 Remote Similarity NPC136188
0.6022 Remote Similarity NPC162742
0.6022 Remote Similarity NPC230301
0.6022 Remote Similarity NPC134847
0.6022 Remote Similarity NPC141071
0.6022 Remote Similarity NPC288035
0.6022 Remote Similarity NPC471723
0.6022 Remote Similarity NPC22105
0.6022 Remote Similarity NPC285893
0.6022 Remote Similarity NPC28657
0.6022 Remote Similarity NPC304309
0.6022 Remote Similarity NPC257347
0.602 Remote Similarity NPC317458
0.602 Remote Similarity NPC474634
0.602 Remote Similarity NPC475789
0.6019 Remote Similarity NPC474001
0.6017 Remote Similarity NPC35037
0.6016 Remote Similarity NPC132847
0.6 Remote Similarity NPC469943
0.6 Remote Similarity NPC477514
0.6 Remote Similarity NPC176621
0.6 Remote Similarity NPC478138
0.6 Remote Similarity NPC475239
0.6 Remote Similarity NPC478137
0.6 Remote Similarity NPC474458
0.6 Remote Similarity NPC473943
0.5982 Remote Similarity NPC307903
0.5982 Remote Similarity NPC140251
0.5979 Remote Similarity NPC474759
0.5979 Remote Similarity NPC474731
0.5979 Remote Similarity NPC474752
0.5979 Remote Similarity NPC474683
0.5979 Remote Similarity NPC82986
0.5979 Remote Similarity NPC47761
0.5979 Remote Similarity NPC7505
0.5979 Remote Similarity NPC4166
0.5963 Remote Similarity NPC476755
0.5962 Remote Similarity NPC476753
0.5962 Remote Similarity NPC476752
0.596 Remote Similarity NPC205845
0.596 Remote Similarity NPC474047
0.596 Remote Similarity NPC185568
0.5957 Remote Similarity NPC107059
0.5957 Remote Similarity NPC300324
0.5957 Remote Similarity NPC129165
0.5957 Remote Similarity NPC321381
0.5957 Remote Similarity NPC113733
0.5957 Remote Similarity NPC321016

  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 NPC166458 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
0.7579 Intermediate Similarity NPD5771 Approved
0.7059 Intermediate Similarity NPD6938 Clinical (unspecified phase)
0.7059 Intermediate Similarity NPD6939 Phase 2
0.7041 Intermediate Similarity NPD5769 Clinical (unspecified phase)
0.6381 Remote Similarity NPD6404 Discontinued
0.6364 Remote Similarity NPD4722 Approved
0.6364 Remote Similarity NPD4723 Approved
0.6222 Remote Similarity NPD4243 Approved
0.6087 Remote Similarity NPD4784 Approved
0.6087 Remote Similarity NPD4785 Approved
0.6044 Remote Similarity NPD5365 Phase 2
0.6022 Remote Similarity NPD7339 Approved
0.6022 Remote Similarity NPD6942 Approved
0.5957 Remote Similarity NPD1346 Approved
0.5946 Remote Similarity NPD7333 Discontinued
0.5851 Remote Similarity NPD4190 Phase 3
0.5851 Remote Similarity NPD5275 Approved
0.5833 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5804 Remote Similarity NPD6640 Phase 3
0.5755 Remote Similarity NPD5707 Approved
0.5714 Remote Similarity NPD7332 Phase 2
0.5714 Remote Similarity NPD7812 Clinical (unspecified phase)
0.5702 Remote Similarity NPD6038 Clinical (unspecified phase)
0.5669 Remote Similarity NPD6914 Discontinued
0.5664 Remote Similarity NPD5717 Approved
0.5652 Remote Similarity NPD6923 Approved
0.5652 Remote Similarity NPD791 Approved
0.5652 Remote Similarity NPD6922 Approved
0.5652 Remote Similarity NPD15 Approved
0.5648 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5631 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5625 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5625 Remote Similarity NPD5103 Approved
0.5619 Remote Similarity NPD4001 Clinical (unspecified phase)
0.5612 Remote Similarity NPD4195 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