Structure

Physi-Chem Properties

Molecular Weight:  456.41
Volume:  518.721
LogP:  6.739
LogD:  5.239
LogS:  -5.29
# Rotatable Bonds:  6
TPSA:  32.34
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.468
Synthetic Accessibility Score:  4.619
Fsp3:  0.9
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.721
MDCK Permeability:  1.2095490092178807e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.313
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.929
30% Bioavailability (F30%):  0.894

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.192
Plasma Protein Binding (PPB):  74.39944458007812%
Volume Distribution (VD):  0.861
Pgp-substrate:  4.247464179992676%

ADMET: Metabolism

CYP1A2-inhibitor:  0.133
CYP1A2-substrate:  0.51
CYP2C19-inhibitor:  0.266
CYP2C19-substrate:  0.96
CYP2C9-inhibitor:  0.421
CYP2C9-substrate:  0.044
CYP2D6-inhibitor:  0.836
CYP2D6-substrate:  0.905
CYP3A4-inhibitor:  0.932
CYP3A4-substrate:  0.847

ADMET: Excretion

Clearance (CL):  13.012
Half-life (T1/2):  0.064

ADMET: Toxicity

hERG Blockers:  0.942
Human Hepatotoxicity (H-HT):  0.448
Drug-inuced Liver Injury (DILI):  0.84
AMES Toxicity:  0.051
Rat Oral Acute Toxicity:  0.927
Maximum Recommended Daily Dose:  0.107
Skin Sensitization:  0.967
Carcinogencity:  0.555
Eye Corrosion:  0.989
Eye Irritation:  0.155
Respiratory Toxicity:  0.926

Download Data

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

  Natural Product: NPC152684

Natural Product ID:  NPC152684
Common Name*:   3,4-Dimethyl-Pent-2-Enoic Acid [(3S,5S,8R,9S,10S,13S,14S,17S)-17-(1-Dimethylamino-Ethyl)-10-Methyl-13-(S)-Methyl-Hexadecahydro-Cyclopenta[A]Phenanthren-3-Yl]-Amide
IUPAC Name:   (E)-N-[(3S,5S,8R,9S,10S,13S,14S,17S)-17-[(1S)-1-(dimethylamino)ethyl]-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yl]-3,4-dimethylpent-2-enamide
Synonyms:  
Standard InCHIKey:  GQPGTQPICSXROA-GGKHHMRBSA-N
Standard InCHI:  InChI=1S/C30H52N2O/c1-19(2)20(3)17-28(33)31-23-13-15-29(5)22(18-23)9-10-24-26-12-11-25(21(4)32(7)8)30(26,6)16-14-27(24)29/h17,19,21-27H,9-16,18H2,1-8H3,(H,31,33)/b20-17+/t21-,22-,23-,24-,25+,26-,27-,29-,30+/m0/s1
SMILES:  OC(=N[C@H]1CC[C@]2([C@H](C1)CC[C@@H]1[C@@H]2CC[C@]2([C@H]1CC[C@@H]2[C@@H](N(C)C)C)C)C)/C=C(/C(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL359415
PubChem CID:   44364861
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
NPT2668 Individual Protein Acetylcholinesterase Torpedo californica IC50 = 50600.0 nM PMID[557446]
NPT2668 Individual Protein Acetylcholinesterase Torpedo californica Ki = 9050.0 nM PMID[557446]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens IC50 = 4630.0 nM PMID[557446]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens Ki = 3250.0 nM PMID[557446]

☑ 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 NPC152684 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
0.9494 High Similarity NPC257962
0.8706 High Similarity NPC166458
0.8101 Intermediate Similarity NPC245223
0.7979 Intermediate Similarity NPC167419
0.7959 Intermediate Similarity NPC55462
0.7927 Intermediate Similarity NPC476904
0.7901 Intermediate Similarity NPC21773
0.7835 Intermediate Similarity NPC471083
0.7835 Intermediate Similarity NPC152718
0.7753 Intermediate Similarity NPC147513
0.7653 Intermediate Similarity NPC50815
0.7653 Intermediate Similarity NPC226509
0.7614 Intermediate Similarity NPC215474
0.76 Intermediate Similarity NPC230677
0.7576 Intermediate Similarity NPC90538
0.7529 Intermediate Similarity NPC7214
0.7526 Intermediate Similarity NPC140685
0.75 Intermediate Similarity NPC469968
0.75 Intermediate Similarity NPC80834
0.75 Intermediate Similarity NPC469958
0.7476 Intermediate Similarity NPC472359
0.7475 Intermediate Similarity NPC247060
0.7473 Intermediate Similarity NPC157479
0.7471 Intermediate Similarity NPC211322
0.747 Intermediate Similarity NPC265789
0.7439 Intermediate Similarity NPC124384
0.7426 Intermediate Similarity NPC36497
0.7353 Intermediate Similarity NPC25340
0.7303 Intermediate Similarity NPC90150
0.7273 Intermediate Similarity NPC275686
0.7222 Intermediate Similarity NPC224072
0.7209 Intermediate Similarity NPC125828
0.7174 Intermediate Similarity NPC311769
0.7174 Intermediate Similarity NPC24733
0.7174 Intermediate Similarity NPC182106
0.7143 Intermediate Similarity NPC171639
0.7143 Intermediate Similarity NPC476903
0.7126 Intermediate Similarity NPC476308
0.7111 Intermediate Similarity NPC118329
0.7111 Intermediate Similarity NPC152039
0.7111 Intermediate Similarity NPC329782
0.7059 Intermediate Similarity NPC476329
0.7059 Intermediate Similarity NPC474583
0.7033 Intermediate Similarity NPC472312
0.7033 Intermediate Similarity NPC283277
0.7033 Intermediate Similarity NPC39966
0.7009 Intermediate Similarity NPC56796
0.7 Intermediate Similarity NPC12035
0.6989 Remote Similarity NPC75810
0.6981 Remote Similarity NPC72753
0.6962 Remote Similarity NPC21781
0.6947 Remote Similarity NPC259252
0.6887 Remote Similarity NPC175585
0.6842 Remote Similarity NPC43308
0.6824 Remote Similarity NPC138409
0.6814 Remote Similarity NPC242692
0.68 Remote Similarity NPC247220
0.6783 Remote Similarity NPC109151
0.6768 Remote Similarity NPC280710
0.6768 Remote Similarity NPC243985
0.6759 Remote Similarity NPC66862
0.6754 Remote Similarity NPC472458
0.6744 Remote Similarity NPC120167
0.6744 Remote Similarity NPC473442
0.6739 Remote Similarity NPC474122
0.6733 Remote Similarity NPC184033
0.6731 Remote Similarity NPC45365
0.6731 Remote Similarity NPC293299
0.6701 Remote Similarity NPC249312
0.67 Remote Similarity NPC272732
0.67 Remote Similarity NPC311164
0.6667 Remote Similarity NPC165396
0.6627 Remote Similarity NPC53276
0.66 Remote Similarity NPC476754
0.6596 Remote Similarity NPC21667
0.6588 Remote Similarity NPC476135
0.6571 Remote Similarity NPC241879
0.6569 Remote Similarity NPC240650
0.6562 Remote Similarity NPC56107
0.6548 Remote Similarity NPC469970
0.6509 Remote Similarity NPC119329
0.6506 Remote Similarity NPC477740
0.6505 Remote Similarity NPC91604
0.65 Remote Similarity NPC476753
0.65 Remote Similarity NPC476752
0.6481 Remote Similarity NPC159367
0.6476 Remote Similarity NPC58200
0.6471 Remote Similarity NPC37792
0.6442 Remote Similarity NPC135799
0.6441 Remote Similarity NPC237286
0.6437 Remote Similarity NPC472831
0.6437 Remote Similarity NPC184919
0.6429 Remote Similarity NPC34754
0.6429 Remote Similarity NPC324405
0.6408 Remote Similarity NPC474164
0.6408 Remote Similarity NPC140300
0.6386 Remote Similarity NPC219621
0.6381 Remote Similarity NPC118275
0.6374 Remote Similarity NPC25110
0.6337 Remote Similarity NPC93027
0.6322 Remote Similarity NPC271640
0.6304 Remote Similarity NPC91665
0.63 Remote Similarity NPC84171
0.6265 Remote Similarity NPC317778
0.6235 Remote Similarity NPC476682
0.6226 Remote Similarity NPC474582
0.6224 Remote Similarity NPC474458
0.6222 Remote Similarity NPC474743
0.6196 Remote Similarity NPC244488
0.6196 Remote Similarity NPC247325
0.619 Remote Similarity NPC132847
0.6168 Remote Similarity NPC176012
0.6168 Remote Similarity NPC476755
0.6154 Remote Similarity NPC289140
0.6147 Remote Similarity NPC86906
0.6145 Remote Similarity NPC309825
0.6111 Remote Similarity NPC3202
0.6091 Remote Similarity NPC46981
0.6071 Remote Similarity NPC328052
0.6055 Remote Similarity NPC212874
0.6042 Remote Similarity NPC475724
0.6024 Remote Similarity NPC472830
0.6024 Remote Similarity NPC324944
0.6 Remote Similarity NPC47982
0.6 Remote Similarity NPC30986
0.6 Remote Similarity NPC209430
0.6 Remote Similarity NPC109546
0.6 Remote Similarity NPC84694
0.6 Remote Similarity NPC143182
0.6 Remote Similarity NPC28862
0.6 Remote Similarity NPC475728
0.6 Remote Similarity NPC474695
0.6 Remote Similarity NPC81306
0.5979 Remote Similarity NPC296701
0.5979 Remote Similarity NPC218616
0.5963 Remote Similarity NPC473254
0.5962 Remote Similarity NPC477290
0.5955 Remote Similarity NPC160209
0.5948 Remote Similarity NPC246904
0.5946 Remote Similarity NPC169375
0.5943 Remote Similarity NPC4834
0.5938 Remote Similarity NPC234193
0.5932 Remote Similarity NPC35037
0.593 Remote Similarity NPC145715
0.5929 Remote Similarity NPC472313
0.5926 Remote Similarity NPC474001
0.5917 Remote Similarity NPC469943
0.5909 Remote Similarity NPC474456
0.5904 Remote Similarity NPC11130
0.5904 Remote Similarity NPC173815
0.5897 Remote Similarity NPC473573
0.5895 Remote Similarity NPC474216
0.5882 Remote Similarity NPC176621
0.5882 Remote Similarity NPC311809
0.5877 Remote Similarity NPC79238
0.5877 Remote Similarity NPC474459
0.5876 Remote Similarity NPC209620
0.5876 Remote Similarity NPC109533
0.5876 Remote Similarity NPC192456
0.5876 Remote Similarity NPC264245
0.5876 Remote Similarity NPC23852
0.5862 Remote Similarity NPC473959
0.5859 Remote Similarity NPC16287
0.5859 Remote Similarity NPC178025
0.5859 Remote Similarity NPC181743
0.5856 Remote Similarity NPC233256
0.5856 Remote Similarity NPC195841
0.5851 Remote Similarity NPC259989
0.5851 Remote Similarity NPC174803
0.5851 Remote Similarity NPC237460
0.5843 Remote Similarity NPC176107
0.5842 Remote Similarity NPC21035
0.5826 Remote Similarity NPC476498
0.5826 Remote Similarity NPC474452
0.5824 Remote Similarity NPC477856
0.5824 Remote Similarity NPC214770
0.5818 Remote Similarity NPC98765
0.5816 Remote Similarity NPC50964
0.5816 Remote Similarity NPC49964
0.5816 Remote Similarity NPC472239
0.5816 Remote Similarity NPC189972
0.5816 Remote Similarity NPC101462
0.5814 Remote Similarity NPC477739
0.5814 Remote Similarity NPC469728
0.581 Remote Similarity NPC473314
0.5804 Remote Similarity NPC244982
0.5804 Remote Similarity NPC476756
0.58 Remote Similarity NPC60350
0.58 Remote Similarity NPC34811
0.5795 Remote Similarity NPC107258
0.5783 Remote Similarity NPC261158
0.5783 Remote Similarity NPC104138
0.5783 Remote Similarity NPC24216
0.5783 Remote Similarity NPC318036
0.5783 Remote Similarity NPC306420
0.5778 Remote Similarity NPC20610
0.5778 Remote Similarity NPC476288
0.5776 Remote Similarity NPC478137
0.5773 Remote Similarity NPC209944
0.5773 Remote Similarity NPC241290

  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 NPC152684 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
0.7849 Intermediate Similarity NPD5771 Approved
0.766 Intermediate Similarity NPD5769 Clinical (unspecified phase)
0.6941 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6941 Remote Similarity NPD6939 Phase 2
0.6132 Remote Similarity NPD6404 Discontinued
0.6111 Remote Similarity NPD5365 Phase 2
0.61 Remote Similarity NPD4723 Approved
0.61 Remote Similarity NPD4722 Approved
0.6066 Remote Similarity NPD6330 Clinical (unspecified phase)
0.6 Remote Similarity NPD2895 Discontinued
0.598 Remote Similarity NPD6934 Discontinued
0.5934 Remote Similarity NPD4243 Approved
0.5856 Remote Similarity NPD7333 Discontinued
0.5833 Remote Similarity NPD7155 Clinical (unspecified phase)
0.5806 Remote Similarity NPD4785 Approved
0.5806 Remote Similarity NPD4784 Approved
0.5745 Remote Similarity NPD7339 Approved
0.5745 Remote Similarity NPD6942 Approved
0.566 Remote Similarity NPD5707 Approved
0.5625 Remote Similarity NPD7812 Clinical (unspecified phase)
0.5612 Remote Similarity NPD7525 Registered

  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