Structure

Physi-Chem Properties

Molecular Weight:  472.37
Volume:  510.449
LogP:  4.326
LogD:  3.444
LogS:  -3.639
# Rotatable Bonds:  4
TPSA:  60.85
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.622
Synthetic Accessibility Score:  5.101
Fsp3:  0.931
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:  -4.815
MDCK Permeability:  1.147397324530175e-05
Pgp-inhibitor:  0.972
Pgp-substrate:  0.104
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.285

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.672
Plasma Protein Binding (PPB):  62.268699645996094%
Volume Distribution (VD):  1.672
Pgp-substrate:  34.44367599487305%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.228
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.957
CYP2C9-inhibitor:  0.062
CYP2C9-substrate:  0.058
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.709
CYP3A4-inhibitor:  0.542
CYP3A4-substrate:  0.812

ADMET: Excretion

Clearance (CL):  20.308
Half-life (T1/2):  0.133

ADMET: Toxicity

hERG Blockers:  0.169
Human Hepatotoxicity (H-HT):  0.353
Drug-inuced Liver Injury (DILI):  0.654
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.482
Maximum Recommended Daily Dose:  0.172
Skin Sensitization:  0.359
Carcinogencity:  0.538
Eye Corrosion:  0.007
Eye Irritation:  0.011
Respiratory Toxicity:  0.975

Download Data

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

  Natural Product: NPC470592

Natural Product ID:  NPC470592
Common Name*:   Terminamine A
IUPAC Name:   (3S)-1-[(3S,5R,8R,9S,10R,13S,14S,16S,17S)-17-[(1S)-1-(dimethylamino)ethyl]-16-hydroxy-10,13-dimethyl-4-oxo-1,2,3,5,6,7,8,9,11,12,14,15,16,17-tetradecahydrocyclopenta[a]phenanthren-3-yl]-3-propan-2-ylazetidin-2-one
Synonyms:   Terminamine A
Standard InCHIKey:  CZSDSCGXOOKZPH-LNOGRUMPSA-N
Standard InCHI:  InChI=1S/C29H48N2O3/c1-16(2)19-15-31(27(19)34)23-11-13-28(4)20-10-12-29(5)22(18(20)8-9-21(28)26(23)33)14-24(32)25(29)17(3)30(6)7/h16-25,32H,8-15H2,1-7H3/t17-,18+,19+,20-,21-,22-,23-,24-,25-,28+,29-/m0/s1
SMILES:  CC(C)C1CN(C1=O)C2CCC3(C4CCC5(C(C4CCC3C2=O)CC(C5C(C)N(C)C)O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2087199
PubChem CID:   70693226
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
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 = 180.0 nM PMID[519160]

☑ 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 NPC470592 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
0.8586 High Similarity NPC292819
0.8404 Intermediate Similarity NPC34811
0.8208 Intermediate Similarity NPC470595
0.8198 Intermediate Similarity NPC474006
0.7925 Intermediate Similarity NPC470596
0.78 Intermediate Similarity NPC312637
0.7586 Intermediate Similarity NPC470593
0.7586 Intermediate Similarity NPC470594
0.757 Intermediate Similarity NPC476755
0.7333 Intermediate Similarity NPC174117
0.729 Intermediate Similarity NPC220111
0.7157 Intermediate Similarity NPC21035
0.7143 Intermediate Similarity NPC244982
0.7143 Intermediate Similarity NPC476756
0.7019 Intermediate Similarity NPC135005
0.7018 Intermediate Similarity NPC473994
0.6947 Remote Similarity NPC310766
0.6915 Remote Similarity NPC473442
0.6915 Remote Similarity NPC120167
0.69 Remote Similarity NPC109533
0.6847 Remote Similarity NPC474001
0.6838 Remote Similarity NPC124358
0.6814 Remote Similarity NPC475239
0.6809 Remote Similarity NPC321732
0.6809 Remote Similarity NPC324607
0.6701 Remote Similarity NPC472854
0.6667 Remote Similarity NPC58057
0.6667 Remote Similarity NPC320549
0.6667 Remote Similarity NPC151018
0.6667 Remote Similarity NPC156277
0.6639 Remote Similarity NPC475340
0.6598 Remote Similarity NPC232112
0.6579 Remote Similarity NPC98765
0.6566 Remote Similarity NPC25110
0.6531 Remote Similarity NPC254340
0.65 Remote Similarity NPC28224
0.6471 Remote Similarity NPC470609
0.6465 Remote Similarity NPC27349
0.6465 Remote Similarity NPC125767
0.6465 Remote Similarity NPC21220
0.6465 Remote Similarity NPC273366
0.6465 Remote Similarity NPC174964
0.6465 Remote Similarity NPC195155
0.6465 Remote Similarity NPC97534
0.6465 Remote Similarity NPC24014
0.6458 Remote Similarity NPC327728
0.6458 Remote Similarity NPC213178
0.6458 Remote Similarity NPC6120
0.6458 Remote Similarity NPC131892
0.6435 Remote Similarity NPC241879
0.6429 Remote Similarity NPC473537
0.641 Remote Similarity NPC8009
0.641 Remote Similarity NPC83047
0.641 Remote Similarity NPC48127
0.641 Remote Similarity NPC267217
0.6408 Remote Similarity NPC469745
0.64 Remote Similarity NPC475742
0.64 Remote Similarity NPC472486
0.64 Remote Similarity NPC472487
0.64 Remote Similarity NPC5767
0.6372 Remote Similarity NPC252564
0.6372 Remote Similarity NPC475249
0.6364 Remote Similarity NPC280026
0.6364 Remote Similarity NPC167702
0.6346 Remote Similarity NPC317066
0.6346 Remote Similarity NPC328007
0.6337 Remote Similarity NPC475031
0.6337 Remote Similarity NPC264602
0.6337 Remote Similarity NPC180199
0.6337 Remote Similarity NPC23884
0.6337 Remote Similarity NPC477919
0.6337 Remote Similarity NPC221420
0.6327 Remote Similarity NPC110615
0.6327 Remote Similarity NPC473267
0.6327 Remote Similarity NPC89310
0.6316 Remote Similarity NPC201712
0.63 Remote Similarity NPC212733
0.6289 Remote Similarity NPC319671
0.6289 Remote Similarity NPC476734
0.6289 Remote Similarity NPC469941
0.6289 Remote Similarity NPC252032
0.6289 Remote Similarity NPC124384
0.6286 Remote Similarity NPC327451
0.6275 Remote Similarity NPC476732
0.6275 Remote Similarity NPC185465
0.6275 Remote Similarity NPC199965
0.627 Remote Similarity NPC238323
0.6261 Remote Similarity NPC475518
0.625 Remote Similarity NPC311164
0.625 Remote Similarity NPC63511
0.625 Remote Similarity NPC272732
0.625 Remote Similarity NPC90150
0.625 Remote Similarity NPC77311
0.625 Remote Similarity NPC139778
0.625 Remote Similarity NPC155985
0.6238 Remote Similarity NPC4209
0.6231 Remote Similarity NPC212106
0.6224 Remote Similarity NPC477929
0.6224 Remote Similarity NPC476731
0.6214 Remote Similarity NPC320144
0.6214 Remote Similarity NPC472310
0.62 Remote Similarity NPC133922
0.6195 Remote Similarity NPC476903
0.6186 Remote Similarity NPC473225
0.6176 Remote Similarity NPC317913
0.6176 Remote Similarity NPC207010
0.6176 Remote Similarity NPC298168
0.6176 Remote Similarity NPC474404
0.6176 Remote Similarity NPC143133
0.6174 Remote Similarity NPC135799
0.6154 Remote Similarity NPC472853
0.6147 Remote Similarity NPC322966
0.614 Remote Similarity NPC184033
0.6139 Remote Similarity NPC472311
0.6139 Remote Similarity NPC159789
0.6132 Remote Similarity NPC245866
0.6132 Remote Similarity NPC323180
0.6122 Remote Similarity NPC245223
0.6121 Remote Similarity NPC77703
0.6117 Remote Similarity NPC80089
0.6117 Remote Similarity NPC324700
0.6117 Remote Similarity NPC34046
0.6117 Remote Similarity NPC224802
0.6117 Remote Similarity NPC171426
0.6111 Remote Similarity NPC476726
0.6111 Remote Similarity NPC476727
0.6111 Remote Similarity NPC474448
0.6095 Remote Similarity NPC192456
0.6083 Remote Similarity NPC476276
0.608 Remote Similarity NPC221196
0.608 Remote Similarity NPC39485
0.6075 Remote Similarity NPC175419
0.6075 Remote Similarity NPC82902
0.6061 Remote Similarity NPC108131
0.6061 Remote Similarity NPC477850
0.6058 Remote Similarity NPC201459
0.6058 Remote Similarity NPC201276
0.6058 Remote Similarity NPC245029
0.6058 Remote Similarity NPC80891
0.6058 Remote Similarity NPC31302
0.6058 Remote Similarity NPC52951
0.6055 Remote Similarity NPC168017
0.6053 Remote Similarity NPC289140
0.605 Remote Similarity NPC36497
0.604 Remote Similarity NPC477930
0.6038 Remote Similarity NPC477858
0.6038 Remote Similarity NPC289486
0.6038 Remote Similarity NPC30583
0.6038 Remote Similarity NPC46881
0.6038 Remote Similarity NPC61107
0.6038 Remote Similarity NPC145143
0.6038 Remote Similarity NPC477935
0.6029 Remote Similarity NPC474210
0.602 Remote Similarity NPC2568
0.602 Remote Similarity NPC260319
0.602 Remote Similarity NPC103647
0.602 Remote Similarity NPC180777
0.602 Remote Similarity NPC474954
0.6019 Remote Similarity NPC182106
0.6019 Remote Similarity NPC147513
0.6019 Remote Similarity NPC477918
0.6019 Remote Similarity NPC311769
0.6019 Remote Similarity NPC474218
0.6 Remote Similarity NPC203170
0.6 Remote Similarity NPC469940
0.5983 Remote Similarity NPC118275
0.5981 Remote Similarity NPC472498
0.5981 Remote Similarity NPC472743
0.5981 Remote Similarity NPC475726
0.5981 Remote Similarity NPC268578
0.5981 Remote Similarity NPC472744
0.5981 Remote Similarity NPC292458
0.5981 Remote Similarity NPC259173
0.5981 Remote Similarity NPC217559
0.5979 Remote Similarity NPC42060
0.5966 Remote Similarity NPC119329
0.5963 Remote Similarity NPC472272
0.5963 Remote Similarity NPC80590
0.5963 Remote Similarity NPC119633
0.5963 Remote Similarity NPC469994
0.5963 Remote Similarity NPC171698
0.5963 Remote Similarity NPC270957
0.5963 Remote Similarity NPC321340
0.5962 Remote Similarity NPC329117
0.596 Remote Similarity NPC474962
0.596 Remote Similarity NPC64466
0.5946 Remote Similarity NPC178632
0.5943 Remote Similarity NPC103754
0.5943 Remote Similarity NPC12933
0.5943 Remote Similarity NPC474484
0.5943 Remote Similarity NPC58631
0.5941 Remote Similarity NPC474123
0.5941 Remote Similarity NPC477229
0.5941 Remote Similarity NPC68426
0.5941 Remote Similarity NPC282905
0.5938 Remote Similarity NPC118937
0.5938 Remote Similarity NPC159654
0.5938 Remote Similarity NPC167995
0.5938 Remote Similarity NPC281540
0.5935 Remote Similarity NPC246399

  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 NPC470592 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
0.7207 Intermediate Similarity NPD6920 Discontinued
0.708 Intermediate Similarity NPD6415 Discontinued
0.7069 Intermediate Similarity NPD8298 Phase 2
0.6915 Remote Similarity NPD4244 Approved
0.6915 Remote Similarity NPD4245 Approved
0.6869 Remote Similarity NPD7155 Clinical (unspecified phase)
0.6809 Remote Similarity NPD3698 Phase 2
0.6792 Remote Similarity NPD6934 Discontinued
0.6757 Remote Similarity NPD8418 Phase 2
0.6667 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6667 Remote Similarity NPD4808 Clinical (unspecified phase)
0.6562 Remote Similarity NPD4789 Approved
0.6552 Remote Similarity NPD7646 Clinical (unspecified phase)
0.6458 Remote Similarity NPD3700 Clinical (unspecified phase)
0.6458 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6429 Remote Similarity NPD7919 Phase 3
0.6429 Remote Similarity NPD7920 Phase 3
0.6383 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6372 Remote Similarity NPD8088 Phase 1
0.6364 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6325 Remote Similarity NPD8040 Discontinued
0.6325 Remote Similarity NPD7333 Discontinued
0.6238 Remote Similarity NPD6117 Approved
0.6228 Remote Similarity NPD3102 Approved
0.6228 Remote Similarity NPD3103 Approved
0.6228 Remote Similarity NPD3104 Approved
0.6228 Remote Similarity NPD3101 Approved
0.6186 Remote Similarity NPD5360 Phase 3
0.6186 Remote Similarity NPD5361 Clinical (unspecified phase)
0.6176 Remote Similarity NPD6116 Phase 1
0.6162 Remote Similarity NPD5777 Approved
0.6154 Remote Similarity NPD7986 Approved
0.6154 Remote Similarity NPD7987 Approved
0.6154 Remote Similarity NPD7911 Approved
0.6154 Remote Similarity NPD7912 Approved
0.6139 Remote Similarity NPD3703 Phase 2
0.6132 Remote Similarity NPD4788 Approved
0.6129 Remote Similarity NPD7755 Approved
0.6129 Remote Similarity NPD7754 Approved
0.6117 Remote Similarity NPD6115 Approved
0.6117 Remote Similarity NPD6114 Approved
0.6117 Remote Similarity NPD6697 Approved
0.6117 Remote Similarity NPD6118 Approved
0.6015 Remote Similarity NPD7751 Phase 1
0.6 Remote Similarity NPD7990 Approved
0.6 Remote Similarity NPD6081 Approved
0.6 Remote Similarity NPD7989 Approved
0.598 Remote Similarity NPD3702 Approved
0.5979 Remote Similarity NPD4224 Phase 2
0.5965 Remote Similarity NPD7991 Discontinued
0.5963 Remote Similarity NPD8308 Discontinued
0.5962 Remote Similarity NPD3671 Phase 1
0.5891 Remote Similarity NPD6909 Approved
0.5891 Remote Similarity NPD6908 Approved
0.5887 Remote Similarity NPD8077 Approved
0.5887 Remote Similarity NPD8078 Approved
0.5877 Remote Similarity NPD2636 Clinical (unspecified phase)
0.5877 Remote Similarity NPD2637 Approved
0.5842 Remote Similarity NPD4758 Discontinued
0.584 Remote Similarity NPD1376 Discontinued
0.578 Remote Similarity NPD3666 Approved
0.578 Remote Similarity NPD3133 Approved
0.578 Remote Similarity NPD4786 Approved
0.578 Remote Similarity NPD3665 Phase 1
0.5776 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5743 Remote Similarity NPD4787 Phase 1
0.5736 Remote Similarity NPD7517 Approved
0.5736 Remote Similarity NPD7519 Approved
0.5736 Remote Similarity NPD7518 Approved
0.5727 Remote Similarity NPD7520 Clinical (unspecified phase)
0.566 Remote Similarity NPD4777 Suspended
0.566 Remote Similarity NPD4776 Phase 2
0.566 Remote Similarity NPD5364 Discontinued
0.563 Remote Similarity NPD5359 Clinical (unspecified phase)
0.5603 Remote Similarity NPD5769 Clinical (unspecified phase)

  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