Structure

Physi-Chem Properties

Molecular Weight:  470.42
Volume:  536.017
LogP:  6.995
LogD:  5.191
LogS:  -5.191
# Rotatable Bonds:  6
TPSA:  23.55
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.403
Synthetic Accessibility Score:  4.76
Fsp3:  0.903
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:  -4.708
MDCK Permeability:  1.2196628631500062e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.432
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.76
30% Bioavailability (F30%):  0.713

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.135
Plasma Protein Binding (PPB):  78.64958953857422%
Volume Distribution (VD):  1.109
Pgp-substrate:  4.008178234100342%

ADMET: Metabolism

CYP1A2-inhibitor:  0.058
CYP1A2-substrate:  0.266
CYP2C19-inhibitor:  0.112
CYP2C19-substrate:  0.98
CYP2C9-inhibitor:  0.31
CYP2C9-substrate:  0.048
CYP2D6-inhibitor:  0.863
CYP2D6-substrate:  0.886
CYP3A4-inhibitor:  0.936
CYP3A4-substrate:  0.914

ADMET: Excretion

Clearance (CL):  13.652
Half-life (T1/2):  0.044

ADMET: Toxicity

hERG Blockers:  0.845
Human Hepatotoxicity (H-HT):  0.362
Drug-inuced Liver Injury (DILI):  0.798
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.833
Maximum Recommended Daily Dose:  0.123
Skin Sensitization:  0.972
Carcinogencity:  0.583
Eye Corrosion:  0.997
Eye Irritation:  0.291
Respiratory Toxicity:  0.894

Download Data

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

  Natural Product: NPC147513

Natural Product ID:  NPC147513
Common Name*:   (E)-3,4-Dimethyl-Pent-2-Enoic Acid [(3S,5S,8R,9S,10S,13S,14S,17S)-17-((S)-1-Dimethylamino-Ethyl)-10,13-Dimethyl-Hexadecahydro-Cyclopenta[A]Phenanthren-3-Yl]-Methyl-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]-N,3,4-trimethylpent-2-enamide
Synonyms:  
Standard InCHIKey:  WCBPBBFIAODRLI-AWUJJIRRSA-N
Standard InCHI:  InChI=1S/C31H54N2O/c1-20(2)21(3)18-29(34)33(9)24-14-16-30(5)23(19-24)10-11-25-27-13-12-26(22(4)32(7)8)31(27,6)17-15-28(25)30/h18,20,22-28H,10-17,19H2,1-9H3/b21-18+/t22-,23-,24-,25-,26+,27-,28-,30-,31+/m0/s1
SMILES:  CC(/C(=C/C(=O)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
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL344593
PubChem CID:   11113449
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
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[12951092]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[12951092]
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]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[15930771]
NPO6711 Streptomyces mirabilis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[19818612]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[9548847]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12328 Ampelopsis japonica Species Vitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12450 Cneorum pulverulentum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12560 Cassia leptophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12328 Ampelopsis japonica Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12328 Ampelopsis japonica Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2332 Plantago serraria Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13128 Crotalaria rosenii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9527 Dendrodoa grossularia Species Styelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12560 Cassia leptophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4160 Cephalosporium polyaleurum Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27888 Sarcococca saligna Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11838 Euphorbia regis-jubae Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7351 Uncaria pteropoda Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6711 Streptomyces mirabilis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12450 Cneorum pulverulentum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12328 Ampelopsis japonica Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18213 Strychnos variabilis Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10911 Euphorbia peplis Species Euphorbiaceae 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 = 6300.0 nM PMID[498315]
NPT2668 Individual Protein Acetylcholinesterase Torpedo californica Ki = 4100.0 nM PMID[498315]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens IC50 = 4070.0 nM PMID[498315]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens Ki = 3400.0 nM PMID[498315]
NPT204 Individual Protein Acetylcholinesterase Homo sapiens IC50 = 6456.54 nM PMID[498316]

☑ 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 NPC147513 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
0.963 High Similarity NPC157479
0.9494 High Similarity NPC90150
0.9136 High Similarity NPC215474
0.8391 Intermediate Similarity NPC43308
0.8228 Intermediate Similarity NPC473442
0.8228 Intermediate Similarity NPC120167
0.7955 Intermediate Similarity NPC182106
0.7955 Intermediate Similarity NPC311769
0.7927 Intermediate Similarity NPC476904
0.7901 Intermediate Similarity NPC21773
0.7753 Intermediate Similarity NPC152684
0.7738 Intermediate Similarity NPC7214
0.7738 Intermediate Similarity NPC25110
0.7692 Intermediate Similarity NPC259252
0.7683 Intermediate Similarity NPC265789
0.7674 Intermediate Similarity NPC211322
0.7528 Intermediate Similarity NPC171639
0.7474 Intermediate Similarity NPC476754
0.7453 Intermediate Similarity NPC246904
0.7416 Intermediate Similarity NPC472312
0.7374 Intermediate Similarity NPC474001
0.7303 Intermediate Similarity NPC257962
0.7303 Intermediate Similarity NPC152039
0.7303 Intermediate Similarity NPC118329
0.7303 Intermediate Similarity NPC329782
0.7209 Intermediate Similarity NPC125828
0.7191 Intermediate Similarity NPC12035
0.7188 Intermediate Similarity NPC93027
0.7188 Intermediate Similarity NPC476752
0.7188 Intermediate Similarity NPC476753
0.7157 Intermediate Similarity NPC476921
0.7129 Intermediate Similarity NPC58200
0.7111 Intermediate Similarity NPC474122
0.7097 Intermediate Similarity NPC166458
0.703 Intermediate Similarity NPC476922
0.7 Intermediate Similarity NPC140685
0.699 Remote Similarity NPC470596
0.6989 Remote Similarity NPC75810
0.6989 Remote Similarity NPC34811
0.6962 Remote Similarity NPC21781
0.6961 Remote Similarity NPC152718
0.6957 Remote Similarity NPC21667
0.6952 Remote Similarity NPC476918
0.6909 Remote Similarity NPC473573
0.6824 Remote Similarity NPC245223
0.68 Remote Similarity NPC476903
0.6796 Remote Similarity NPC226509
0.6792 Remote Similarity NPC470595
0.6762 Remote Similarity NPC476926
0.6752 Remote Similarity NPC79698
0.6733 Remote Similarity NPC184033
0.6701 Remote Similarity NPC249312
0.6667 Remote Similarity NPC63511
0.6667 Remote Similarity NPC469958
0.6636 Remote Similarity NPC476920
0.6636 Remote Similarity NPC476919
0.6632 Remote Similarity NPC24733
0.6628 Remote Similarity NPC138409
0.6628 Remote Similarity NPC124384
0.6627 Remote Similarity NPC53276
0.6604 Remote Similarity NPC86906
0.6604 Remote Similarity NPC230677
0.6604 Remote Similarity NPC476328
0.6602 Remote Similarity NPC477964
0.6588 Remote Similarity NPC176107
0.6548 Remote Similarity NPC469970
0.6522 Remote Similarity NPC127430
0.6522 Remote Similarity NPC120699
0.6514 Remote Similarity NPC472313
0.6489 Remote Similarity NPC283277
0.6481 Remote Similarity NPC159367
0.6481 Remote Similarity NPC476276
0.6475 Remote Similarity NPC126458
0.6471 Remote Similarity NPC92327
0.6465 Remote Similarity NPC84171
0.6455 Remote Similarity NPC143173
0.6449 Remote Similarity NPC55462
0.6423 Remote Similarity NPC473962
0.6408 Remote Similarity NPC167419
0.6404 Remote Similarity NPC474006
0.6396 Remote Similarity NPC469968
0.6396 Remote Similarity NPC80834
0.6396 Remote Similarity NPC474452
0.6386 Remote Similarity NPC219621
0.6381 Remote Similarity NPC474582
0.6381 Remote Similarity NPC77703
0.6374 Remote Similarity NPC476308
0.6373 Remote Similarity NPC311164
0.6373 Remote Similarity NPC272732
0.6364 Remote Similarity NPC35734
0.6364 Remote Similarity NPC159577
0.6364 Remote Similarity NPC282593
0.6354 Remote Similarity NPC116881
0.6354 Remote Similarity NPC57163
0.6346 Remote Similarity NPC91604
0.6322 Remote Similarity NPC271640
0.6321 Remote Similarity NPC476755
0.6321 Remote Similarity NPC50815
0.6321 Remote Similarity NPC471083
0.6311 Remote Similarity NPC247220
0.6306 Remote Similarity NPC474459
0.6306 Remote Similarity NPC79238
0.6304 Remote Similarity NPC308050
0.6296 Remote Similarity NPC474695
0.6292 Remote Similarity NPC476329
0.6292 Remote Similarity NPC115023
0.6286 Remote Similarity NPC135799
0.6286 Remote Similarity NPC275686
0.6265 Remote Similarity NPC317778
0.6264 Remote Similarity NPC293803
0.6262 Remote Similarity NPC241879
0.625 Remote Similarity NPC474164
0.625 Remote Similarity NPC140300
0.625 Remote Similarity NPC292819
0.6239 Remote Similarity NPC25340
0.6222 Remote Similarity NPC303613
0.6222 Remote Similarity NPC251705
0.6222 Remote Similarity NPC474228
0.6186 Remote Similarity NPC135639
0.6186 Remote Similarity NPC61321
0.6186 Remote Similarity NPC143344
0.6186 Remote Similarity NPC78058
0.6186 Remote Similarity NPC234822
0.6186 Remote Similarity NPC207048
0.618 Remote Similarity NPC477856
0.618 Remote Similarity NPC307176
0.618 Remote Similarity NPC214770
0.6168 Remote Similarity NPC247060
0.6147 Remote Similarity NPC195841
0.6147 Remote Similarity NPC36497
0.6147 Remote Similarity NPC233256
0.6136 Remote Similarity NPC20610
0.6126 Remote Similarity NPC175585
0.6111 Remote Similarity NPC110615
0.6111 Remote Similarity NPC90538
0.6111 Remote Similarity NPC234707
0.6092 Remote Similarity NPC176171
0.6092 Remote Similarity NPC37792
0.6087 Remote Similarity NPC255650
0.6075 Remote Similarity NPC118275
0.6071 Remote Similarity NPC472359
0.6067 Remote Similarity NPC139397
0.6067 Remote Similarity NPC182815
0.6067 Remote Similarity NPC184919
0.6047 Remote Similarity NPC206660
0.6044 Remote Similarity NPC470044
0.6044 Remote Similarity NPC470045
0.6024 Remote Similarity NPC472830
0.6024 Remote Similarity NPC324944
0.6022 Remote Similarity NPC69408
0.6022 Remote Similarity NPC259989
0.6022 Remote Similarity NPC474463
0.6022 Remote Similarity NPC174803
0.6019 Remote Similarity NPC176012
0.6019 Remote Similarity NPC470592
0.6019 Remote Similarity NPC247316
0.6 Remote Similarity NPC289140
0.6 Remote Similarity NPC265782
0.6 Remote Similarity NPC2634
0.6 Remote Similarity NPC40574
0.6 Remote Similarity NPC251929
0.6 Remote Similarity NPC260040
0.5978 Remote Similarity NPC309852
0.5978 Remote Similarity NPC255021
0.5965 Remote Similarity NPC56796
0.5965 Remote Similarity NPC124358
0.5963 Remote Similarity NPC474583
0.596 Remote Similarity NPC76283
0.5946 Remote Similarity NPC46981
0.5946 Remote Similarity NPC244982
0.5946 Remote Similarity NPC476756
0.5938 Remote Similarity NPC474509
0.5934 Remote Similarity NPC470078
0.5934 Remote Similarity NPC54123
0.5934 Remote Similarity NPC305501
0.5917 Remote Similarity NPC472458
0.5909 Remote Similarity NPC119329
0.5909 Remote Similarity NPC475239
0.5909 Remote Similarity NPC212874
0.5904 Remote Similarity NPC173815
0.59 Remote Similarity NPC56107
0.5897 Remote Similarity NPC477121
0.5895 Remote Similarity NPC105197
0.5851 Remote Similarity NPC320667
0.5851 Remote Similarity NPC214125
0.5843 Remote Similarity NPC476135
0.5833 Remote Similarity NPC190211
0.5833 Remote Similarity NPC242692
0.5833 Remote Similarity NPC239768
0.5833 Remote Similarity NPC60772
0.5833 Remote Similarity NPC128698
0.5833 Remote Similarity NPC268580
0.5825 Remote Similarity NPC473056
0.5818 Remote Similarity NPC98765
0.5814 Remote Similarity NPC477461
0.5814 Remote Similarity NPC252684
0.5814 Remote Similarity NPC477459
0.581 Remote Similarity NPC243985
0.581 Remote Similarity NPC280710
0.5806 Remote Similarity NPC329866

  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 NPC147513 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
0.7079 Intermediate Similarity NPD7155 Clinical (unspecified phase)
0.6477 Remote Similarity NPD5365 Phase 2
0.6465 Remote Similarity NPD6934 Discontinued
0.6296 Remote Similarity NPD7333 Discontinued
0.6275 Remote Similarity NPD5769 Clinical (unspecified phase)
0.618 Remote Similarity NPD4747 Approved
0.6117 Remote Similarity NPD5771 Approved
0.6067 Remote Similarity NPD4137 Phase 3
0.6 Remote Similarity NPD4691 Approved
0.6 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6 Remote Similarity NPD6939 Phase 2
0.5978 Remote Similarity NPD5733 Approved
0.5806 Remote Similarity NPD4058 Approved
0.5806 Remote Similarity NPD4687 Approved
0.5778 Remote Similarity NPD3621 Clinical (unspecified phase)
0.5761 Remote Similarity NPD816 Approved
0.5761 Remote Similarity NPD815 Approved
0.5761 Remote Similarity NPD5276 Approved
0.5758 Remote Similarity NPD3527 Clinical (unspecified phase)
0.569 Remote Similarity NPD8078 Approved
0.569 Remote Similarity NPD8077 Approved
0.567 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