Structure

Physi-Chem Properties

Molecular Weight:  456.37
Volume:  501.659
LogP:  5.468
LogD:  4.826
LogS:  -5.301
# Rotatable Bonds:  3
TPSA:  43.78
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.474
Synthetic Accessibility Score:  4.955
Fsp3:  0.897
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:  -4.89
MDCK Permeability:  8.765153324929997e-06
Pgp-inhibitor:  0.991
Pgp-substrate:  0.261
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.15
30% Bioavailability (F30%):  0.932

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.194
Plasma Protein Binding (PPB):  72.99803924560547%
Volume Distribution (VD):  1.073
Pgp-substrate:  8.407550811767578%

ADMET: Metabolism

CYP1A2-inhibitor:  0.051
CYP1A2-substrate:  0.4
CYP2C19-inhibitor:  0.114
CYP2C19-substrate:  0.964
CYP2C9-inhibitor:  0.112
CYP2C9-substrate:  0.074
CYP2D6-inhibitor:  0.599
CYP2D6-substrate:  0.872
CYP3A4-inhibitor:  0.823
CYP3A4-substrate:  0.88

ADMET: Excretion

Clearance (CL):  9.659
Half-life (T1/2):  0.132

ADMET: Toxicity

hERG Blockers:  0.609
Human Hepatotoxicity (H-HT):  0.401
Drug-inuced Liver Injury (DILI):  0.885
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.784
Maximum Recommended Daily Dose:  0.214
Skin Sensitization:  0.948
Carcinogencity:  0.352
Eye Corrosion:  0.201
Eye Irritation:  0.018
Respiratory Toxicity:  0.977

Download Data

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

  Natural Product: NPC470596

Natural Product ID:  NPC470596
Common Name*:   Terminamine E
IUPAC Name:   1-[(3R,4R,5R,8S,9S,10R,13S,14S,17S)-17-[(1S)-1-(dimethylamino)ethyl]-4-hydroxy-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-propan-2-ylideneazetidin-2-one
Synonyms:   terminamine E
Standard InCHIKey:  ZHEKCAHHEJODEA-WXWFEBHUSA-N
Standard InCHI:  InChI=1S/C29H48N2O2/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/h18-19,21-26,32H,8-16H2,1-7H3/t18-,19-,21+,22-,23-,24-,25+,26+,28+,29+/m0/s1
SMILES:  CN([C@H]([C@H]1CC[C@@H]2[C@]1(C)CC[C@H]1[C@H]2CC[C@@H]2[C@]1(C)CC[C@H]([C@@H]2O)N1CC(=C(C)C)C1=O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2087203
PubChem CID:   70682697
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001295] Hydroxysteroids

*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
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[22804108]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13852 Pachysandra terminalis 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
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 = 70.0 nM PMID[537044]

☑ 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 NPC470596 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
0.9697 High Similarity NPC470595
0.9175 High Similarity NPC292819
0.7925 Intermediate Similarity NPC470592
0.7607 Intermediate Similarity NPC470594
0.7607 Intermediate Similarity NPC470593
0.729 Intermediate Similarity NPC476903
0.7288 Intermediate Similarity NPC474006
0.7273 Intermediate Similarity NPC90150
0.713 Intermediate Similarity NPC289140
0.71 Intermediate Similarity NPC109533
0.708 Intermediate Similarity NPC36497
0.708 Intermediate Similarity NPC55462
0.6991 Remote Similarity NPC475239
0.699 Remote Similarity NPC34811
0.699 Remote Similarity NPC147513
0.6981 Remote Similarity NPC312637
0.6964 Remote Similarity NPC476755
0.6957 Remote Similarity NPC159367
0.6903 Remote Similarity NPC241879
0.687 Remote Similarity NPC25340
0.6864 Remote Similarity NPC124358
0.6847 Remote Similarity NPC220111
0.6833 Remote Similarity NPC165396
0.6814 Remote Similarity NPC471083
0.678 Remote Similarity NPC66862
0.6771 Remote Similarity NPC120167
0.6771 Remote Similarity NPC473442
0.6762 Remote Similarity NPC157479
0.6723 Remote Similarity NPC469968
0.6723 Remote Similarity NPC56796
0.6723 Remote Similarity NPC80834
0.6695 Remote Similarity NPC72753
0.6695 Remote Similarity NPC472359
0.6609 Remote Similarity NPC474583
0.6607 Remote Similarity NPC473537
0.6583 Remote Similarity NPC474452
0.6581 Remote Similarity NPC244982
0.6581 Remote Similarity NPC476756
0.6577 Remote Similarity NPC174117
0.6555 Remote Similarity NPC472313
0.6549 Remote Similarity NPC252564
0.6549 Remote Similarity NPC475249
0.6545 Remote Similarity NPC93027
0.6542 Remote Similarity NPC21035
0.6525 Remote Similarity NPC476276
0.6522 Remote Similarity NPC50815
0.65 Remote Similarity NPC474459
0.6496 Remote Similarity NPC86906
0.6491 Remote Similarity NPC201712
0.6471 Remote Similarity NPC473994
0.646 Remote Similarity NPC140300
0.6436 Remote Similarity NPC25110
0.6435 Remote Similarity NPC474001
0.6435 Remote Similarity NPC475518
0.6435 Remote Similarity NPC77703
0.6429 Remote Similarity NPC242692
0.6393 Remote Similarity NPC478137
0.6389 Remote Similarity NPC43308
0.6381 Remote Similarity NPC215474
0.6379 Remote Similarity NPC247060
0.6378 Remote Similarity NPC472458
0.6356 Remote Similarity NPC476328
0.6341 Remote Similarity NPC145501
0.6303 Remote Similarity NPC46981
0.6283 Remote Similarity NPC311164
0.6283 Remote Similarity NPC272732
0.6281 Remote Similarity NPC63511
0.6271 Remote Similarity NPC476921
0.6262 Remote Similarity NPC175419
0.6261 Remote Similarity NPC91604
0.623 Remote Similarity NPC79238
0.6207 Remote Similarity NPC135799
0.6204 Remote Similarity NPC75810
0.6179 Remote Similarity NPC476498
0.6174 Remote Similarity NPC474164
0.6168 Remote Similarity NPC323180
0.6167 Remote Similarity NPC8009
0.6167 Remote Similarity NPC169375
0.6167 Remote Similarity NPC48127
0.6167 Remote Similarity NPC267217
0.6167 Remote Similarity NPC83047
0.6162 Remote Similarity NPC124384
0.6148 Remote Similarity NPC328052
0.6147 Remote Similarity NPC270957
0.6147 Remote Similarity NPC171698
0.6147 Remote Similarity NPC321340
0.6147 Remote Similarity NPC119633
0.6142 Remote Similarity NPC475340
0.6132 Remote Similarity NPC192456
0.6126 Remote Similarity NPC323156
0.6126 Remote Similarity NPC135005
0.6107 Remote Similarity NPC237286
0.6102 Remote Similarity NPC176012
0.6093 Remote Similarity NPC73644
0.6091 Remote Similarity NPC89747
0.608 Remote Similarity NPC476499
0.6068 Remote Similarity NPC477964
0.6068 Remote Similarity NPC275686
0.6055 Remote Similarity NPC182106
0.6055 Remote Similarity NPC311769
0.605 Remote Similarity NPC98765
0.6045 Remote Similarity NPC478139
0.6031 Remote Similarity NPC321197
0.6017 Remote Similarity NPC118275
0.6016 Remote Similarity NPC287764
0.6016 Remote Similarity NPC139778
0.6 Remote Similarity NPC245223
0.6 Remote Similarity NPC212874
0.6 Remote Similarity NPC155985
0.5984 Remote Similarity NPC476918
0.5981 Remote Similarity NPC257962
0.598 Remote Similarity NPC232112
0.5969 Remote Similarity NPC208118
0.5969 Remote Similarity NPC96080
0.5969 Remote Similarity NPC99905
0.5946 Remote Similarity NPC473525
0.594 Remote Similarity NPC96010
0.594 Remote Similarity NPC317654
0.5935 Remote Similarity NPC218602
0.5929 Remote Similarity NPC126993
0.5917 Remote Similarity NPC90538
0.5909 Remote Similarity NPC22133
0.5909 Remote Similarity NPC76518
0.5897 Remote Similarity NPC240650
0.5897 Remote Similarity NPC91036
0.5897 Remote Similarity NPC184033
0.5896 Remote Similarity NPC476497
0.5893 Remote Similarity NPC259252
0.5882 Remote Similarity NPC151018
0.5882 Remote Similarity NPC320549
0.5882 Remote Similarity NPC58057
0.5882 Remote Similarity NPC156277
0.5882 Remote Similarity NPC111234
0.5877 Remote Similarity NPC74296
0.5877 Remote Similarity NPC272746
0.5877 Remote Similarity NPC110923
0.5876 Remote Similarity NPC114891
0.5873 Remote Similarity NPC28224
0.5872 Remote Similarity NPC472743
0.5872 Remote Similarity NPC475726
0.5872 Remote Similarity NPC246956
0.5868 Remote Similarity NPC119329
0.5865 Remote Similarity NPC21220
0.5865 Remote Similarity NPC240235
0.5865 Remote Similarity NPC195155
0.5865 Remote Similarity NPC104387
0.5865 Remote Similarity NPC70982
0.5865 Remote Similarity NPC174964
0.5865 Remote Similarity NPC178383
0.5865 Remote Similarity NPC97534
0.5865 Remote Similarity NPC273366
0.5865 Remote Similarity NPC212733
0.5865 Remote Similarity NPC230704
0.5865 Remote Similarity NPC3403
0.5865 Remote Similarity NPC185536
0.5865 Remote Similarity NPC212879
0.5865 Remote Similarity NPC125767
0.5865 Remote Similarity NPC231256
0.5859 Remote Similarity NPC142712
0.5856 Remote Similarity NPC471737
0.5856 Remote Similarity NPC269396
0.5856 Remote Similarity NPC98236
0.5856 Remote Similarity NPC323958
0.5856 Remote Similarity NPC322672
0.5856 Remote Similarity NPC72133
0.5849 Remote Similarity NPC244385
0.5849 Remote Similarity NPC138621
0.5849 Remote Similarity NPC167037
0.5849 Remote Similarity NPC6978
0.5849 Remote Similarity NPC285761
0.5841 Remote Similarity NPC472240
0.5841 Remote Similarity NPC262858
0.5833 Remote Similarity NPC152718
0.5826 Remote Similarity NPC476304
0.5826 Remote Similarity NPC12722
0.5821 Remote Similarity NPC476501
0.582 Remote Similarity NPC233256
0.582 Remote Similarity NPC476926
0.582 Remote Similarity NPC195841
0.5818 Remote Similarity NPC214043
0.5818 Remote Similarity NPC475745
0.5818 Remote Similarity NPC474482
0.5818 Remote Similarity NPC74595
0.5818 Remote Similarity NPC33913
0.5818 Remote Similarity NPC472265
0.5818 Remote Similarity NPC264665
0.5818 Remote Similarity NPC85774
0.5814 Remote Similarity NPC475887
0.581 Remote Similarity NPC472487
0.581 Remote Similarity NPC5767
0.581 Remote Similarity NPC86305
0.581 Remote Similarity NPC472486
0.581 Remote Similarity NPC91573
0.581 Remote Similarity NPC78067
0.581 Remote Similarity NPC14112
0.581 Remote Similarity NPC93662
0.581 Remote Similarity NPC237460
0.581 Remote Similarity NPC4209
0.581 Remote Similarity NPC475742
0.581 Remote Similarity NPC278091

  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 NPC470596 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
0.693 Remote Similarity NPD6920 Discontinued
0.681 Remote Similarity NPD6415 Discontinued
0.6724 Remote Similarity NPD7646 Clinical (unspecified phase)
0.6694 Remote Similarity NPD7754 Approved
0.6694 Remote Similarity NPD7755 Approved
0.6667 Remote Similarity NPD8298 Phase 2
0.6607 Remote Similarity NPD7920 Phase 3
0.6607 Remote Similarity NPD7919 Phase 3
0.6549 Remote Similarity NPD8088 Phase 1
0.6446 Remote Similarity NPD8078 Approved
0.6446 Remote Similarity NPD8077 Approved
0.6356 Remote Similarity NPD8040 Discontinued
0.6348 Remote Similarity NPD8418 Phase 2
0.6325 Remote Similarity NPD7911 Approved
0.6325 Remote Similarity NPD7987 Approved
0.6325 Remote Similarity NPD7912 Approved
0.6325 Remote Similarity NPD7986 Approved
0.6218 Remote Similarity NPD7333 Discontinued
0.6167 Remote Similarity NPD7990 Approved
0.6167 Remote Similarity NPD7989 Approved
0.6095 Remote Similarity NPD7155 Clinical (unspecified phase)
0.6071 Remote Similarity NPD6934 Discontinued
0.6 Remote Similarity NPD8308 Discontinued
0.6 Remote Similarity NPD1376 Discontinued
0.5923 Remote Similarity NPD6908 Approved
0.5923 Remote Similarity NPD6909 Approved
0.5882 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5882 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5862 Remote Similarity NPD7991 Discontinued
0.5841 Remote Similarity NPD5328 Approved
0.581 Remote Similarity NPD6117 Approved
0.5794 Remote Similarity NPD7335 Phase 2
0.5794 Remote Similarity NPD7337 Clinical (unspecified phase)
0.5794 Remote Similarity NPD7336 Phase 2
0.5769 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5766 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5755 Remote Similarity NPD6116 Phase 1
0.5755 Remote Similarity NPD8143 Approved
0.5755 Remote Similarity NPD8144 Approved
0.5741 Remote Similarity NPD7525 Registered
0.5739 Remote Similarity NPD6079 Approved
0.5714 Remote Similarity NPD3618 Phase 1
0.5701 Remote Similarity NPD6115 Approved
0.5701 Remote Similarity NPD6118 Approved
0.5701 Remote Similarity NPD6114 Approved
0.5701 Remote Similarity NPD6697 Approved
0.5686 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5686 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5686 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5678 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5641 Remote Similarity NPD5771 Approved
0.5639 Remote Similarity NPD7652 Discontinued
0.5631 Remote Similarity NPD4244 Approved
0.5631 Remote Similarity NPD4789 Approved
0.5631 Remote Similarity NPD4245 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