Structure

Physi-Chem Properties

Molecular Weight:  388.35
Volume:  434.878
LogP:  4.945
LogD:  4.295
LogS:  -2.304
# Rotatable Bonds:  4
TPSA:  32.34
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.729
Synthetic Accessibility Score:  4.473
Fsp3:  0.96
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:  -4.707
MDCK Permeability:  1.1094575711467769e-05
Pgp-inhibitor:  0.996
Pgp-substrate:  0.498
Human Intestinal Absorption (HIA):  0.039
20% Bioavailability (F20%):  0.564
30% Bioavailability (F30%):  0.96

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.3
Plasma Protein Binding (PPB):  50.82401657104492%
Volume Distribution (VD):  1.022
Pgp-substrate:  26.591506958007812%

ADMET: Metabolism

CYP1A2-inhibitor:  0.127
CYP1A2-substrate:  0.464
CYP2C19-inhibitor:  0.143
CYP2C19-substrate:  0.909
CYP2C9-inhibitor:  0.034
CYP2C9-substrate:  0.045
CYP2D6-inhibitor:  0.034
CYP2D6-substrate:  0.65
CYP3A4-inhibitor:  0.763
CYP3A4-substrate:  0.704

ADMET: Excretion

Clearance (CL):  7.784
Half-life (T1/2):  0.118

ADMET: Toxicity

hERG Blockers:  0.451
Human Hepatotoxicity (H-HT):  0.735
Drug-inuced Liver Injury (DILI):  0.825
AMES Toxicity:  0.299
Rat Oral Acute Toxicity:  0.835
Maximum Recommended Daily Dose:  0.697
Skin Sensitization:  0.964
Carcinogencity:  0.641
Eye Corrosion:  0.023
Eye Irritation:  0.021
Respiratory Toxicity:  0.943

Download Data

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

  Natural Product: NPC25110

Natural Product ID:  NPC25110
Common Name*:   N-Methyl-N-[1-((3S,5S,8R,9S,10S,13S,14S,17S)-10-Methyl-13-(S)-Methyl-3-Methylamino-Hexadecahydro-Cyclopenta[A]Phenanthren-17-Yl)-Ethyl]-Acetamide
IUPAC Name:   N-[(1S)-1-[(3S,5S,8R,9S,10S,13S,14S,17S)-10,13-dimethyl-3-(methylamino)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]ethyl]-N-methylacetamide
Synonyms:  
Standard InCHIKey:  WRFQFEGHCJALCO-MENSBAHOSA-N
Standard InCHI:  InChI=1S/C25H44N2O/c1-16(27(6)17(2)28)21-9-10-22-20-8-7-18-15-19(26-5)11-13-24(18,3)23(20)12-14-25(21,22)4/h16,18-23,26H,7-15H2,1-6H3/t16-,18-,19-,20-,21+,22-,23-,24-,25+/m0/s1
SMILES:  C[C@@H]([C@H]1CC[C@H]2[C@@H]3CC[C@H]4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)NC)N(C)C(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL147346
PubChem CID:   44364863
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 = 204200.0 nM PMID[476076]
NPT2668 Individual Protein Acetylcholinesterase Torpedo californica Ki = 216000.0 nM PMID[476076]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens IC50 = 16500.0 nM PMID[476076]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens Ki = 8600.0 nM PMID[476076]

☑ 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 NPC25110 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
0.9286 High Similarity NPC473442
0.9286 High Similarity NPC120167
0.8642 High Similarity NPC43308
0.8571 High Similarity NPC469970
0.8429 Intermediate Similarity NPC53276
0.8219 Intermediate Similarity NPC271640
0.8125 Intermediate Similarity NPC90150
0.7857 Intermediate Similarity NPC21781
0.7738 Intermediate Similarity NPC34811
0.7738 Intermediate Similarity NPC147513
0.7662 Intermediate Similarity NPC110615
0.7632 Intermediate Similarity NPC245223
0.759 Intermediate Similarity NPC215474
0.7442 Intermediate Similarity NPC157479
0.7403 Intermediate Similarity NPC124384
0.7108 Intermediate Similarity NPC39308
0.7024 Intermediate Similarity NPC211322
0.6966 Remote Similarity NPC21035
0.686 Remote Similarity NPC329782
0.686 Remote Similarity NPC152039
0.686 Remote Similarity NPC118329
0.6842 Remote Similarity NPC292819
0.6813 Remote Similarity NPC323156
0.6782 Remote Similarity NPC472312
0.6744 Remote Similarity NPC12035
0.6667 Remote Similarity NPC257962
0.6596 Remote Similarity NPC476753
0.6596 Remote Similarity NPC476752
0.6566 Remote Similarity NPC58200
0.6566 Remote Similarity NPC470592
0.6526 Remote Similarity NPC476754
0.6495 Remote Similarity NPC473537
0.6458 Remote Similarity NPC174117
0.6436 Remote Similarity NPC470596
0.6429 Remote Similarity NPC252564
0.6429 Remote Similarity NPC476904
0.6429 Remote Similarity NPC475249
0.641 Remote Similarity NPC477740
0.6386 Remote Similarity NPC21773
0.6374 Remote Similarity NPC152684
0.6374 Remote Similarity NPC182106
0.6374 Remote Similarity NPC311769
0.6364 Remote Similarity NPC201712
0.6333 Remote Similarity NPC21667
0.6301 Remote Similarity NPC472828
0.63 Remote Similarity NPC475518
0.6292 Remote Similarity NPC474122
0.6279 Remote Similarity NPC7214
0.6277 Remote Similarity NPC135005
0.6264 Remote Similarity NPC116881
0.6264 Remote Similarity NPC57163
0.625 Remote Similarity NPC470595
0.6196 Remote Similarity NPC24733
0.619 Remote Similarity NPC473994
0.617 Remote Similarity NPC259252
0.6139 Remote Similarity NPC474001
0.6111 Remote Similarity NPC109533
0.6042 Remote Similarity NPC312637
0.6019 Remote Similarity NPC124358
0.6 Remote Similarity NPC474027
0.6 Remote Similarity NPC244982
0.6 Remote Similarity NPC476756
0.6 Remote Similarity NPC265789
0.6 Remote Similarity NPC474435
0.5981 Remote Similarity NPC472313
0.5981 Remote Similarity NPC72753
0.5978 Remote Similarity NPC153734
0.5978 Remote Similarity NPC171639
0.596 Remote Similarity NPC155985
0.5957 Remote Similarity NPC56107
0.5926 Remote Similarity NPC66862
0.5926 Remote Similarity NPC79238
0.5926 Remote Similarity NPC474459
0.5905 Remote Similarity NPC230677
0.589 Remote Similarity NPC201713
0.5882 Remote Similarity NPC135799
0.5876 Remote Similarity NPC84171
0.5872 Remote Similarity NPC474452
0.587 Remote Similarity NPC283277
0.5856 Remote Similarity NPC246904
0.5842 Remote Similarity NPC474164
0.5804 Remote Similarity NPC473573
0.5795 Remote Similarity NPC125828
0.5794 Remote Similarity NPC159367
0.5784 Remote Similarity NPC140685
0.5758 Remote Similarity NPC93027
0.5755 Remote Similarity NPC195841
0.5755 Remote Similarity NPC233256
0.5738 Remote Similarity NPC126458
0.5733 Remote Similarity NPC212905
0.573 Remote Similarity NPC259989
0.573 Remote Similarity NPC174803
0.5714 Remote Similarity NPC184819
0.5702 Remote Similarity NPC475340
0.5686 Remote Similarity NPC167419
0.5684 Remote Similarity NPC75810
0.5682 Remote Similarity NPC17770
0.5679 Remote Similarity NPC477739
0.5673 Remote Similarity NPC118275
0.5652 Remote Similarity NPC470594
0.5652 Remote Similarity NPC470593
0.5647 Remote Similarity NPC476288
0.5641 Remote Similarity NPC143597
0.5641 Remote Similarity NPC151464
0.5631 Remote Similarity NPC220111
0.5625 Remote Similarity NPC166458
0.5619 Remote Similarity NPC476755
0.5619 Remote Similarity NPC176012
0.5618 Remote Similarity NPC477002
0.561 Remote Similarity NPC89921
0.5607 Remote Similarity NPC36497

  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 NPC25110 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
0.7875 Intermediate Similarity NPD7155 Clinical (unspecified phase)
0.7111 Intermediate Similarity NPD6934 Discontinued
0.6744 Remote Similarity NPD3155 Clinical (unspecified phase)
0.6495 Remote Similarity NPD7920 Phase 3
0.6495 Remote Similarity NPD7919 Phase 3
0.6484 Remote Similarity NPD8308 Discontinued
0.6429 Remote Similarity NPD8088 Phase 1
0.6389 Remote Similarity NPD3721 Approved
0.6389 Remote Similarity NPD3722 Approved
0.6143 Remote Similarity NPD872 Approved
0.6143 Remote Similarity NPD874 Approved
0.6136 Remote Similarity NPD4776 Phase 2
0.6136 Remote Similarity NPD4777 Suspended
0.6053 Remote Similarity NPD628 Phase 3
0.6053 Remote Similarity NPD625 Approved
0.6053 Remote Similarity NPD627 Approved
0.6053 Remote Similarity NPD626 Phase 3
0.602 Remote Similarity NPD2636 Clinical (unspecified phase)
0.602 Remote Similarity NPD2637 Approved
0.6 Remote Similarity NPD3727 Discontinued
0.589 Remote Similarity NPD4834 Discontinued
0.5814 Remote Similarity NPD5365 Phase 2
0.5714 Remote Similarity NPD7987 Approved
0.5714 Remote Similarity NPD7911 Approved
0.5714 Remote Similarity NPD7986 Approved
0.5714 Remote Similarity NPD7912 Approved
0.5634 Remote Similarity NPD873 Approved
0.5634 Remote Similarity NPD871 Approved
0.5631 Remote Similarity NPD3104 Approved
0.5631 Remote Similarity NPD3101 Approved
0.5631 Remote Similarity NPD3103 Approved
0.5631 Remote Similarity NPD3102 Approved
0.5616 Remote Similarity NPD5379 Clinical (unspecified phase)
0.5607 Remote Similarity NPD6920 Discontinued
0.5607 Remote Similarity NPD8040 Discontinued
0.56 Remote Similarity NPD5793 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