Structure

Physi-Chem Properties

Molecular Weight:  454.36
Volume:  499.022
LogP:  5.402
LogD:  4.696
LogS:  -5.419
# Rotatable Bonds:  4
TPSA:  40.62
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.535
Synthetic Accessibility Score:  5.01
Fsp3:  0.862
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.754
MDCK Permeability:  1.3455935004458297e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.362
30% Bioavailability (F30%):  0.483

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.351
Plasma Protein Binding (PPB):  84.43489837646484%
Volume Distribution (VD):  1.014
Pgp-substrate:  5.939655780792236%

ADMET: Metabolism

CYP1A2-inhibitor:  0.056
CYP1A2-substrate:  0.387
CYP2C19-inhibitor:  0.106
CYP2C19-substrate:  0.97
CYP2C9-inhibitor:  0.309
CYP2C9-substrate:  0.073
CYP2D6-inhibitor:  0.538
CYP2D6-substrate:  0.881
CYP3A4-inhibitor:  0.9
CYP3A4-substrate:  0.897

ADMET: Excretion

Clearance (CL):  15.876
Half-life (T1/2):  0.031

ADMET: Toxicity

hERG Blockers:  0.645
Human Hepatotoxicity (H-HT):  0.315
Drug-inuced Liver Injury (DILI):  0.799
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.762
Maximum Recommended Daily Dose:  0.141
Skin Sensitization:  0.945
Carcinogencity:  0.598
Eye Corrosion:  0.004
Eye Irritation:  0.011
Respiratory Toxicity:  0.978

Download Data

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

  Natural Product: NPC474001

Natural Product ID:  NPC474001
Common Name*:   (+)-(20S)-20-(Dimethylamino)-3-(3'alpha-Isopropyl)-Lactam-5Alpha-Pregn-2-En-4-One
IUPAC Name:   (3R)-1-[(5R,8S,9S,10R,13S,14S,17S)-17-[(1S)-1-(dimethylamino)ethyl]-10,13-dimethyl-4-oxo-1,5,6,7,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-3-yl]-3-propan-2-ylazetidin-2-one
Synonyms:  
Standard InCHIKey:  IVYPSBIZZDNZBC-JUFXZFBXSA-N
Standard InCHI:  InChI=1S/C29H46N2O2/c1-17(2)20-16-31(27(20)33)25-13-15-29(5)23-12-14-28(4)21(18(3)30(6)7)10-11-22(28)19(23)8-9-24(29)26(25)32/h13,17-24H,8-12,14-16H2,1-7H3/t18-,19-,20-,21+,22-,23-,24-,28+,29+/m0/s1
SMILES:  CC(C)C1CN(C1=O)C2=CCC3(C4CCC5(C(C4CCC3C2=O)CCC5C(C)N(C)C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL457817
PubChem CID:   44584022
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001194] Oxosteroids

*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
NPO4994 Pachysandra procumbens Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[9784163]
NPO4994 Pachysandra procumbens 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
NPT3844 Protein Complex Anti-estrogen binding site (AEBS) Homo sapiens IC50 = 2800.0 nM PMID[514711]

☑ 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 NPC474001 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
0.8611 High Similarity NPC474006
0.83 Intermediate Similarity NPC184033
0.7917 Intermediate Similarity NPC34811
0.783 Intermediate Similarity NPC469958
0.7732 Intermediate Similarity NPC311769
0.7732 Intermediate Similarity NPC182106
0.7604 Intermediate Similarity NPC215474
0.75 Intermediate Similarity NPC259252
0.7477 Intermediate Similarity NPC152718
0.7374 Intermediate Similarity NPC147513
0.7315 Intermediate Similarity NPC226509
0.73 Intermediate Similarity NPC157479
0.7232 Intermediate Similarity NPC175585
0.7196 Intermediate Similarity NPC140685
0.7156 Intermediate Similarity NPC58200
0.7117 Intermediate Similarity NPC230677
0.7064 Intermediate Similarity NPC34193
0.7048 Intermediate Similarity NPC476753
0.7048 Intermediate Similarity NPC476752
0.7 Intermediate Similarity NPC21667
0.6991 Remote Similarity NPC24596
0.6991 Remote Similarity NPC476918
0.6981 Remote Similarity NPC476754
0.697 Remote Similarity NPC90150
0.6964 Remote Similarity NPC476328
0.6923 Remote Similarity NPC249312
0.6915 Remote Similarity NPC305501
0.6847 Remote Similarity NPC470592
0.6842 Remote Similarity NPC474228
0.6842 Remote Similarity NPC303613
0.6842 Remote Similarity NPC476276
0.6814 Remote Similarity NPC476926
0.6814 Remote Similarity NPC185929
0.6771 Remote Similarity NPC255021
0.6737 Remote Similarity NPC234707
0.6724 Remote Similarity NPC63511
0.6697 Remote Similarity NPC247220
0.6667 Remote Similarity NPC143173
0.6667 Remote Similarity NPC477964
0.6667 Remote Similarity NPC251705
0.6633 Remote Similarity NPC69408
0.6632 Remote Similarity NPC35734
0.6632 Remote Similarity NPC307176
0.6632 Remote Similarity NPC159577
0.6632 Remote Similarity NPC282593
0.6632 Remote Similarity NPC265782
0.6632 Remote Similarity NPC2634
0.6632 Remote Similarity NPC251929
0.6598 Remote Similarity NPC309852
0.6581 Remote Similarity NPC72688
0.6579 Remote Similarity NPC476921
0.6562 Remote Similarity NPC115023
0.6562 Remote Similarity NPC54123
0.6562 Remote Similarity NPC21773
0.6538 Remote Similarity NPC76283
0.6531 Remote Similarity NPC293803
0.6531 Remote Similarity NPC255650
0.6526 Remote Similarity NPC139397
0.6495 Remote Similarity NPC470045
0.6495 Remote Similarity NPC470044
0.6465 Remote Similarity NPC7214
0.646 Remote Similarity NPC77703
0.6458 Remote Similarity NPC120167
0.6458 Remote Similarity NPC473442
0.6458 Remote Similarity NPC260040
0.6435 Remote Similarity NPC475239
0.6435 Remote Similarity NPC470596
0.6429 Remote Similarity NPC476904
0.6422 Remote Similarity NPC93027
0.6422 Remote Similarity NPC247316
0.6421 Remote Similarity NPC20610
0.6415 Remote Similarity NPC43308
0.641 Remote Similarity NPC476919
0.641 Remote Similarity NPC476920
0.6392 Remote Similarity NPC265789
0.6373 Remote Similarity NPC474509
0.6364 Remote Similarity NPC176336
0.6354 Remote Similarity NPC182815
0.6289 Remote Similarity NPC40574
0.6275 Remote Similarity NPC90965
0.6275 Remote Similarity NPC170793
0.6271 Remote Similarity NPC470595
0.6263 Remote Similarity NPC474796
0.6263 Remote Similarity NPC329866
0.6263 Remote Similarity NPC474797
0.626 Remote Similarity NPC473573
0.625 Remote Similarity NPC472239
0.625 Remote Similarity NPC100297
0.6239 Remote Similarity NPC233256
0.6239 Remote Similarity NPC195841
0.6226 Remote Similarity NPC75810
0.6224 Remote Similarity NPC223187
0.6224 Remote Similarity NPC470078
0.6224 Remote Similarity NPC5701
0.6211 Remote Similarity NPC323005
0.62 Remote Similarity NPC473171
0.6195 Remote Similarity NPC292819
0.6168 Remote Similarity NPC322672
0.6154 Remote Similarity NPC79698
0.6154 Remote Similarity NPC118329
0.6154 Remote Similarity NPC152039
0.6146 Remote Similarity NPC176107
0.6139 Remote Similarity NPC25110
0.6122 Remote Similarity NPC477856
0.6122 Remote Similarity NPC214770
0.6111 Remote Similarity NPC473525
0.6102 Remote Similarity NPC86906
0.6095 Remote Similarity NPC320514
0.6095 Remote Similarity NPC3511
0.6095 Remote Similarity NPC472867
0.6095 Remote Similarity NPC142253
0.6091 Remote Similarity NPC473056
0.6082 Remote Similarity NPC260474
0.6082 Remote Similarity NPC188292
0.6075 Remote Similarity NPC29447
0.6075 Remote Similarity NPC319913
0.6068 Remote Similarity NPC98765
0.6061 Remote Similarity NPC225467
0.6061 Remote Similarity NPC190035
0.6058 Remote Similarity NPC12035
0.6048 Remote Similarity NPC246904
0.6042 Remote Similarity NPC92327
0.604 Remote Similarity NPC125828
0.6038 Remote Similarity NPC171639
0.602 Remote Similarity NPC256846
0.602 Remote Similarity NPC477857
0.6019 Remote Similarity NPC469996
0.6019 Remote Similarity NPC470052
0.6019 Remote Similarity NPC166458
0.6019 Remote Similarity NPC82635
0.6017 Remote Similarity NPC119329
0.6 Remote Similarity NPC329782
0.6 Remote Similarity NPC212210
0.6 Remote Similarity NPC474122
0.6 Remote Similarity NPC477121
0.5983 Remote Similarity NPC476755
0.5981 Remote Similarity NPC178025
0.5981 Remote Similarity NPC214043
0.5981 Remote Similarity NPC16287
0.5981 Remote Similarity NPC85774
0.5981 Remote Similarity NPC181743
0.5981 Remote Similarity NPC87552
0.598 Remote Similarity NPC469793
0.598 Remote Similarity NPC469796
0.598 Remote Similarity NPC474463
0.5971 Remote Similarity NPC153007
0.5963 Remote Similarity NPC93778
0.596 Remote Similarity NPC328895
0.5948 Remote Similarity NPC239768
0.5948 Remote Similarity NPC128698
0.5946 Remote Similarity NPC47230
0.5946 Remote Similarity NPC17143
0.5943 Remote Similarity NPC472312
0.5943 Remote Similarity NPC193347
0.5935 Remote Similarity NPC124358
0.5926 Remote Similarity NPC126458
0.5926 Remote Similarity NPC8571
0.5926 Remote Similarity NPC60350
0.5926 Remote Similarity NPC152684
0.5926 Remote Similarity NPC469948
0.5922 Remote Similarity NPC470557
0.5922 Remote Similarity NPC91665
0.5918 Remote Similarity NPC87141
0.5918 Remote Similarity NPC310992
0.5905 Remote Similarity NPC472478
0.5905 Remote Similarity NPC250632
0.5902 Remote Similarity NPC328052
0.59 Remote Similarity NPC181204
0.59 Remote Similarity NPC110615
0.5897 Remote Similarity NPC476922
0.5895 Remote Similarity NPC165695
0.5888 Remote Similarity NPC41539
0.5882 Remote Similarity NPC473962
0.5872 Remote Similarity NPC474733
0.5872 Remote Similarity NPC145879
0.5872 Remote Similarity NPC474732
0.5872 Remote Similarity NPC474778
0.5872 Remote Similarity NPC31564
0.5865 Remote Similarity NPC228911
0.5865 Remote Similarity NPC119326
0.5865 Remote Similarity NPC115515
0.5859 Remote Similarity NPC286814
0.5856 Remote Similarity NPC262043
0.5854 Remote Similarity NPC79238
0.5849 Remote Similarity NPC147066
0.5849 Remote Similarity NPC477372
0.5833 Remote Similarity NPC475124
0.5833 Remote Similarity NPC78058
0.5833 Remote Similarity NPC143344
0.5833 Remote Similarity NPC234822
0.5833 Remote Similarity NPC473246
0.5833 Remote Similarity NPC61321
0.5833 Remote Similarity NPC469662
0.5833 Remote Similarity NPC135639
0.5833 Remote Similarity NPC237712
0.5833 Remote Similarity NPC144258
0.5826 Remote Similarity NPC476903
0.5818 Remote Similarity NPC475740
0.5818 Remote Similarity NPC136948
0.5818 Remote Similarity NPC476293

  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 NPC474001 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
0.6832 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6632 Remote Similarity NPD4747 Approved
0.6632 Remote Similarity NPD4691 Approved
0.66 Remote Similarity NPD7155 Clinical (unspecified phase)
0.6526 Remote Similarity NPD4137 Phase 3
0.6514 Remote Similarity NPD5769 Clinical (unspecified phase)
0.6429 Remote Similarity NPD5733 Approved
0.6429 Remote Similarity NPD4058 Approved
0.6379 Remote Similarity NPD7333 Discontinued
0.6263 Remote Similarity NPD4687 Approved
0.6239 Remote Similarity NPD6934 Discontinued
0.6224 Remote Similarity NPD5276 Approved
0.6154 Remote Similarity NPD8028 Phase 2
0.6106 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6082 Remote Similarity NPD3621 Clinical (unspecified phase)
0.5943 Remote Similarity NPD4223 Phase 3
0.5943 Remote Similarity NPD4221 Approved
0.5926 Remote Similarity NPD5329 Approved
0.5833 Remote Similarity NPD4197 Approved
0.5814 Remote Similarity NPD6908 Approved
0.5814 Remote Similarity NPD6909 Approved
0.5766 Remote Similarity NPD5737 Approved
0.5766 Remote Similarity NPD6672 Approved
0.576 Remote Similarity NPD1376 Discontinued
0.5752 Remote Similarity NPD6079 Approved
0.575 Remote Similarity NPD7812 Clinical (unspecified phase)
0.5727 Remote Similarity NPD5205 Approved
0.5727 Remote Similarity NPD7334 Approved
0.5727 Remote Similarity NPD4138 Approved
0.5727 Remote Similarity NPD5330 Approved
0.5727 Remote Similarity NPD6684 Approved
0.5727 Remote Similarity NPD6409 Approved
0.5727 Remote Similarity NPD4693 Phase 3
0.5727 Remote Similarity NPD7146 Approved
0.5727 Remote Similarity NPD4690 Approved
0.5727 Remote Similarity NPD3574 Clinical (unspecified phase)
0.5727 Remote Similarity NPD4689 Approved
0.5727 Remote Similarity NPD5690 Phase 2
0.5727 Remote Similarity NPD4688 Approved
0.5727 Remote Similarity NPD7521 Approved
0.5714 Remote Similarity NPD6673 Approved
0.5714 Remote Similarity NPD6904 Approved
0.5714 Remote Similarity NPD6080 Approved
0.5714 Remote Similarity NPD5328 Approved
0.5714 Remote Similarity NPD3617 Approved
0.5693 Remote Similarity NPD2754 Discontinued
0.5688 Remote Similarity NPD3666 Approved
0.5688 Remote Similarity NPD4786 Approved
0.5688 Remote Similarity NPD3133 Approved
0.5688 Remote Similarity NPD3665 Phase 1
0.5678 Remote Similarity NPD6404 Discontinued
0.5664 Remote Similarity NPD4096 Approved
0.5625 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6903 Approved
0.5625 Remote Similarity NPD5208 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