Structure

Physi-Chem Properties

Molecular Weight:  632.44
Volume:  664.045
LogP:  4.662
LogD:  4.33
LogS:  -4.64
# Rotatable Bonds:  10
TPSA:  116.61
# H-Bond Aceptor:  9
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.303
Synthetic Accessibility Score:  5.683
Fsp3:  0.917
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.176
MDCK Permeability:  5.098744804854505e-05
Pgp-inhibitor:  0.998
Pgp-substrate:  0.983
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.106

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.109
Plasma Protein Binding (PPB):  71.7347640991211%
Volume Distribution (VD):  0.775
Pgp-substrate:  30.63524055480957%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.062
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.936
CYP2C9-inhibitor:  0.056
CYP2C9-substrate:  0.055
CYP2D6-inhibitor:  0.042
CYP2D6-substrate:  0.176
CYP3A4-inhibitor:  0.627
CYP3A4-substrate:  0.769

ADMET: Excretion

Clearance (CL):  9.624
Half-life (T1/2):  0.492

ADMET: Toxicity

hERG Blockers:  0.395
Human Hepatotoxicity (H-HT):  0.464
Drug-inuced Liver Injury (DILI):  0.898
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.664
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.434
Carcinogencity:  0.295
Eye Corrosion:  0.004
Eye Irritation:  0.012
Respiratory Toxicity:  0.961

Download Data

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

  Natural Product: NPC470594

Natural Product ID:  NPC470594
Common Name*:   Terminamine C
IUPAC Name:   [(1R,3S,4R,5R,8S,9S,10S,11R,13S,14S,16S,17S)-1-acetyloxy-17-[(1S)-1-(dimethylamino)ethyl]-4,16-dihydroxy-10,13-dimethyl-3-[(3S)-2-oxo-3-propan-2-ylazetidin-1-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-11-yl] 3-methylbutanoate
Synonyms:   Terminamine C
Standard InCHIKey:  SUPKERYLYKAVRS-KIYBVETFSA-N
Standard InCHI:  InChI=1S/C36H60N2O7/c1-18(2)13-30(41)45-28-16-35(7)25(14-27(40)31(35)20(5)37(9)10)22-11-12-24-33(42)26(38-17-23(19(3)4)34(38)43)15-29(44-21(6)39)36(24,8)32(22)28/h18-20,22-29,31-33,40,42H,11-17H2,1-10H3/t20-,22-,23+,24-,25-,26-,27-,28+,29+,31-,32+,33+,35-,36+/m0/s1
SMILES:  CC(=O)O[C@@H]1C[C@H](N2C[C@@H](C2=O)C(C)C)[C@@H]([C@H]2[C@@]1(C)[C@H]1[C@H](OC(=O)CC(C)C)C[C@]3([C@H]([C@@H]1CC2)C[C@@H]([C@@H]3[C@@H](N(C)C)C)O)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2087201
PubChem CID:   70697321
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001295] Hydroxysteroids
          • [CHEMONTID:0003229] 16-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 = 80.0 nM PMID[475970]

☑ 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 NPC470594 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
1.0 High Similarity NPC470593
0.8182 Intermediate Similarity NPC292819
0.7863 Intermediate Similarity NPC470595
0.7607 Intermediate Similarity NPC470596
0.7586 Intermediate Similarity NPC470592
0.7462 Intermediate Similarity NPC476497
0.7385 Intermediate Similarity NPC476501
0.7273 Intermediate Similarity NPC309249
0.7197 Intermediate Similarity NPC212106
0.719 Intermediate Similarity NPC83047
0.719 Intermediate Similarity NPC267217
0.719 Intermediate Similarity NPC48127
0.719 Intermediate Similarity NPC8009
0.7154 Intermediate Similarity NPC139778
0.7143 Intermediate Similarity NPC476502
0.7054 Intermediate Similarity NPC208118
0.7054 Intermediate Similarity NPC96080
0.7054 Intermediate Similarity NPC99905
0.7031 Intermediate Similarity NPC475887
0.6875 Remote Similarity NPC165396
0.687 Remote Similarity NPC476504
0.6835 Remote Similarity NPC474210
0.6833 Remote Similarity NPC201712
0.6765 Remote Similarity NPC476967
0.6718 Remote Similarity NPC475340
0.6716 Remote Similarity NPC476503
0.6667 Remote Similarity NPC473994
0.6667 Remote Similarity NPC473537
0.6612 Remote Similarity NPC252564
0.6612 Remote Similarity NPC475249
0.6589 Remote Similarity NPC28224
0.6504 Remote Similarity NPC475518
0.65 Remote Similarity NPC262050
0.6493 Remote Similarity NPC242692
0.6486 Remote Similarity NPC476176
0.6444 Remote Similarity NPC472458
0.6441 Remote Similarity NPC312637
0.6429 Remote Similarity NPC36497
0.6396 Remote Similarity NPC471045
0.6391 Remote Similarity NPC474006
0.6385 Remote Similarity NPC124358
0.6379 Remote Similarity NPC171698
0.6379 Remote Similarity NPC270957
0.6379 Remote Similarity NPC119633
0.6379 Remote Similarity NPC321340
0.6372 Remote Similarity NPC73515
0.6372 Remote Similarity NPC109533
0.6364 Remote Similarity NPC476955
0.6341 Remote Similarity NPC220111
0.6316 Remote Similarity NPC39485
0.6316 Remote Similarity NPC221196
0.6303 Remote Similarity NPC77756
0.6293 Remote Similarity NPC34811
0.6293 Remote Similarity NPC266651
0.6271 Remote Similarity NPC203170
0.627 Remote Similarity NPC241879
0.625 Remote Similarity NPC52756
0.6231 Remote Similarity NPC287764
0.6207 Remote Similarity NPC471044
0.6207 Remote Similarity NPC175419
0.6207 Remote Similarity NPC473336
0.6198 Remote Similarity NPC476189
0.6195 Remote Similarity NPC220379
0.6195 Remote Similarity NPC80891
0.6195 Remote Similarity NPC201276
0.6186 Remote Similarity NPC21035
0.6183 Remote Similarity NPC66862
0.6179 Remote Similarity NPC476903
0.6172 Remote Similarity NPC86906
0.6161 Remote Similarity NPC212453
0.6143 Remote Similarity NPC470537
0.6143 Remote Similarity NPC280903
0.614 Remote Similarity NPC474714
0.6121 Remote Similarity NPC323180
0.6121 Remote Similarity NPC477285
0.6121 Remote Similarity NPC111582
0.6116 Remote Similarity NPC473066
0.6115 Remote Similarity NPC321197
0.6107 Remote Similarity NPC72753
0.6106 Remote Similarity NPC171426
0.6106 Remote Similarity NPC80089
0.6106 Remote Similarity NPC34046
0.6106 Remote Similarity NPC224802
0.6106 Remote Similarity NPC324700
0.6102 Remote Similarity NPC155531
0.6102 Remote Similarity NPC215968
0.6102 Remote Similarity NPC472272
0.6098 Remote Similarity NPC155985
0.6098 Remote Similarity NPC174117
0.6071 Remote Similarity NPC237286
0.6063 Remote Similarity NPC476755
0.6061 Remote Similarity NPC474459
0.6061 Remote Similarity NPC246399
0.6061 Remote Similarity NPC34977
0.6048 Remote Similarity NPC116683
0.6048 Remote Similarity NPC289140
0.6045 Remote Similarity NPC476499
0.6034 Remote Similarity NPC477286
0.6034 Remote Similarity NPC202688
0.6034 Remote Similarity NPC286719
0.6034 Remote Similarity NPC154043
0.6034 Remote Similarity NPC60018
0.6034 Remote Similarity NPC121121
0.6018 Remote Similarity NPC317913
0.6018 Remote Similarity NPC207010
0.6015 Remote Similarity NPC80834
0.6015 Remote Similarity NPC469968
0.6015 Remote Similarity NPC474452
0.6014 Remote Similarity NPC238323
0.6 Remote Similarity NPC261616
0.6 Remote Similarity NPC322966
0.6 Remote Similarity NPC317534
0.5969 Remote Similarity NPC475239
0.5966 Remote Similarity NPC477283
0.5963 Remote Similarity NPC73644
0.595 Remote Similarity NPC323156
0.5948 Remote Similarity NPC469745
0.5948 Remote Similarity NPC190940
0.594 Remote Similarity NPC79238
0.5935 Remote Similarity NPC182740
0.5935 Remote Similarity NPC122083
0.5935 Remote Similarity NPC211845
0.5935 Remote Similarity NPC256104
0.5932 Remote Similarity NPC473299
0.5929 Remote Similarity NPC4209
0.5929 Remote Similarity NPC473477
0.592 Remote Similarity NPC304899
0.592 Remote Similarity NPC296936
0.592 Remote Similarity NPC156377
0.592 Remote Similarity NPC253115
0.5917 Remote Similarity NPC5943
0.5913 Remote Similarity NPC477287
0.5909 Remote Similarity NPC63588
0.5909 Remote Similarity NPC120167
0.5909 Remote Similarity NPC232925
0.5909 Remote Similarity NPC251201
0.5909 Remote Similarity NPC473442
0.5906 Remote Similarity NPC108371
0.5902 Remote Similarity NPC53890
0.5902 Remote Similarity NPC123252
0.5902 Remote Similarity NPC219937
0.5902 Remote Similarity NPC194485
0.5897 Remote Similarity NPC289486
0.5897 Remote Similarity NPC470611
0.5897 Remote Similarity NPC61107
0.5897 Remote Similarity NPC296734
0.5896 Remote Similarity NPC476498
0.589 Remote Similarity NPC477072
0.5887 Remote Similarity NPC470424
0.5877 Remote Similarity NPC476233
0.5877 Remote Similarity NPC171658
0.5873 Remote Similarity NPC470591
0.5873 Remote Similarity NPC471241
0.5868 Remote Similarity NPC201607
0.5868 Remote Similarity NPC56777
0.5868 Remote Similarity NPC160304
0.5865 Remote Similarity NPC472359
0.5865 Remote Similarity NPC472313
0.5856 Remote Similarity NPC252182
0.5856 Remote Similarity NPC470071
0.5856 Remote Similarity NPC1340
0.5856 Remote Similarity NPC187471
0.5854 Remote Similarity NPC130840
0.5852 Remote Similarity NPC478137
0.5846 Remote Similarity NPC327093
0.5841 Remote Similarity NPC212733
0.5841 Remote Similarity NPC186851
0.584 Remote Similarity NPC305808
0.584 Remote Similarity NPC287354
0.584 Remote Similarity NPC21897
0.584 Remote Similarity NPC62407
0.5833 Remote Similarity NPC471240
0.5833 Remote Similarity NPC114378
0.5833 Remote Similarity NPC103782
0.5833 Remote Similarity NPC323958
0.5833 Remote Similarity NPC131365
0.5827 Remote Similarity NPC292775
0.582 Remote Similarity NPC135005
0.5818 Remote Similarity NPC477820
0.5814 Remote Similarity NPC233274
0.5814 Remote Similarity NPC287638
0.5814 Remote Similarity NPC194750
0.5814 Remote Similarity NPC213528
0.5814 Remote Similarity NPC244969
0.5812 Remote Similarity NPC58631
0.5809 Remote Similarity NPC145501
0.5809 Remote Similarity NPC470540
0.5806 Remote Similarity NPC26046
0.5806 Remote Similarity NPC472231
0.5806 Remote Similarity NPC161035
0.5806 Remote Similarity NPC472232
0.5804 Remote Similarity NPC470610
0.5802 Remote Similarity NPC231530
0.5802 Remote Similarity NPC278628
0.5802 Remote Similarity NPC306776
0.5798 Remote Similarity NPC319909
0.5798 Remote Similarity NPC299963
0.5794 Remote Similarity NPC476728
0.5785 Remote Similarity NPC239938
0.5781 Remote Similarity NPC208358

  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 NPC470594 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
0.7479 Intermediate Similarity NPD7646 Clinical (unspecified phase)
0.7395 Intermediate Similarity NPD8040 Discontinued
0.7227 Intermediate Similarity NPD7987 Approved
0.7227 Intermediate Similarity NPD7911 Approved
0.7227 Intermediate Similarity NPD7912 Approved
0.7227 Intermediate Similarity NPD7986 Approved
0.7143 Intermediate Similarity NPD7755 Approved
0.7143 Intermediate Similarity NPD7754 Approved
0.7119 Intermediate Similarity NPD8418 Phase 2
0.7049 Intermediate Similarity NPD7990 Approved
0.7049 Intermediate Similarity NPD7989 Approved
0.6984 Remote Similarity NPD8298 Phase 2
0.6923 Remote Similarity NPD7991 Discontinued
0.6905 Remote Similarity NPD8077 Approved
0.6905 Remote Similarity NPD8078 Approved
0.6829 Remote Similarity NPD6920 Discontinued
0.6667 Remote Similarity NPD7919 Phase 3
0.6667 Remote Similarity NPD7920 Phase 3
0.6612 Remote Similarity NPD8088 Phase 1
0.6587 Remote Similarity NPD6415 Discontinued
0.6379 Remote Similarity NPD8308 Discontinued
0.6328 Remote Similarity NPD8174 Phase 2
0.6106 Remote Similarity NPD6114 Approved
0.6106 Remote Similarity NPD6115 Approved
0.6106 Remote Similarity NPD6118 Approved
0.6106 Remote Similarity NPD6697 Approved
0.6018 Remote Similarity NPD8144 Approved
0.6018 Remote Similarity NPD6116 Phase 1
0.6018 Remote Similarity NPD8143 Approved
0.6 Remote Similarity NPD6940 Discontinued
0.5929 Remote Similarity NPD6117 Approved
0.5899 Remote Similarity NPD6909 Approved
0.5899 Remote Similarity NPD6908 Approved
0.5878 Remote Similarity NPD8307 Discontinued
0.5878 Remote Similarity NPD8140 Approved
0.5752 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5745 Remote Similarity NPD7652 Discontinued
0.5726 Remote Similarity NPD6928 Phase 2
0.5685 Remote Similarity NPD7751 Phase 1
0.5674 Remote Similarity NPD6921 Approved
0.563 Remote Similarity NPD8087 Discontinued
0.5625 Remote Similarity NPD3715 Approved
0.5625 Remote Similarity NPD3713 Approved
0.5625 Remote Similarity NPD3714 Approved
0.5603 Remote Similarity NPD8346 Approved
0.5603 Remote Similarity NPD8347 Approved
0.5603 Remote Similarity NPD8345 Approved
0.56 Remote Similarity NPD8035 Phase 2
0.56 Remote Similarity NPD8034 Phase 2

  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