Structure

Physi-Chem Properties

Molecular Weight:  472.37
Volume:  510.449
LogP:  4.446
LogD:  4.567
LogS:  -4.67
# Rotatable Bonds:  3
TPSA:  64.01
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.48
Synthetic Accessibility Score:  5.162
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:  -4.948
MDCK Permeability:  8.541249371774029e-06
Pgp-inhibitor:  0.988
Pgp-substrate:  0.864
Human Intestinal Absorption (HIA):  0.201
20% Bioavailability (F20%):  0.056
30% Bioavailability (F30%):  0.903

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.248
Plasma Protein Binding (PPB):  63.66255569458008%
Volume Distribution (VD):  1.093
Pgp-substrate:  25.4757080078125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.032
CYP1A2-substrate:  0.321
CYP2C19-inhibitor:  0.034
CYP2C19-substrate:  0.951
CYP2C9-inhibitor:  0.038
CYP2C9-substrate:  0.061
CYP2D6-inhibitor:  0.078
CYP2D6-substrate:  0.644
CYP3A4-inhibitor:  0.621
CYP3A4-substrate:  0.826

ADMET: Excretion

Clearance (CL):  9.915
Half-life (T1/2):  0.505

ADMET: Toxicity

hERG Blockers:  0.222
Human Hepatotoxicity (H-HT):  0.381
Drug-inuced Liver Injury (DILI):  0.822
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.808
Maximum Recommended Daily Dose:  0.251
Skin Sensitization:  0.922
Carcinogencity:  0.373
Eye Corrosion:  0.13
Eye Irritation:  0.024
Respiratory Toxicity:  0.981

Download Data

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

  Natural Product: NPC470595

Natural Product ID:  NPC470595
Common Name*:   Terminamine D
IUPAC Name:   1-[(3R,4R,5R,8R,9S,10R,13S,14S,16S,17S)-17-[(1S)-1-(dimethylamino)ethyl]-4,16-dihydroxy-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 D
Standard InCHIKey:  VSNSBSZXWOFUMA-VAYDHFJYSA-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/h17-18,20-26,32-33H,8-15H2,1-7H3/t17-,18+,20-,21-,22-,23+,24-,25-,26+,28+,29-/m0/s1
SMILES:  CC(C1C(CC2C1(CCC3C2CCC4C3(CCC(C4O)N5CC(=C(C)C)C5=O)C)C)O)N(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2087202
PubChem CID:   70697322
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 = 200.0 nM PMID[507103]

☑ 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 NPC470595 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 NPC470596
0.89 High Similarity NPC292819
0.8208 Intermediate Similarity NPC470592
0.7863 Intermediate Similarity NPC470593
0.7863 Intermediate Similarity NPC470594
0.7542 Intermediate Similarity NPC474006
0.7168 Intermediate Similarity NPC241879
0.7091 Intermediate Similarity NPC476903
0.708 Intermediate Similarity NPC476755
0.7059 Intermediate Similarity NPC90150
0.6937 Remote Similarity NPC289140
0.6897 Remote Similarity NPC36497
0.6897 Remote Similarity NPC55462
0.6893 Remote Similarity NPC109533
0.6822 Remote Similarity NPC21035
0.681 Remote Similarity NPC475239
0.6792 Remote Similarity NPC34811
0.6792 Remote Similarity NPC147513
0.6789 Remote Similarity NPC312637
0.678 Remote Similarity NPC159367
0.6695 Remote Similarity NPC25340
0.6695 Remote Similarity NPC244982
0.6695 Remote Similarity NPC476756
0.6694 Remote Similarity NPC124358
0.6667 Remote Similarity NPC165396
0.6667 Remote Similarity NPC220111
0.6638 Remote Similarity NPC471083
0.6612 Remote Similarity NPC66862
0.6574 Remote Similarity NPC157479
0.6566 Remote Similarity NPC473442
0.6566 Remote Similarity NPC120167
0.6557 Remote Similarity NPC80834
0.6557 Remote Similarity NPC56796
0.6557 Remote Similarity NPC469968
0.6549 Remote Similarity NPC311164
0.6549 Remote Similarity NPC272732
0.6529 Remote Similarity NPC472359
0.6529 Remote Similarity NPC72753
0.6471 Remote Similarity NPC86906
0.6466 Remote Similarity NPC135799
0.6441 Remote Similarity NPC474583
0.6435 Remote Similarity NPC473537
0.6423 Remote Similarity NPC474452
0.6417 Remote Similarity NPC48127
0.6417 Remote Similarity NPC83047
0.6417 Remote Similarity NPC267217
0.6417 Remote Similarity NPC8009
0.6404 Remote Similarity NPC174117
0.6393 Remote Similarity NPC472313
0.6379 Remote Similarity NPC475249
0.6379 Remote Similarity NPC252564
0.6372 Remote Similarity NPC93027
0.6364 Remote Similarity NPC476276
0.6356 Remote Similarity NPC50815
0.6341 Remote Similarity NPC474459
0.6325 Remote Similarity NPC201712
0.6311 Remote Similarity NPC473994
0.6293 Remote Similarity NPC140300
0.6291 Remote Similarity NPC73644
0.6279 Remote Similarity NPC242692
0.6271 Remote Similarity NPC118275
0.6271 Remote Similarity NPC474001
0.6271 Remote Similarity NPC475518
0.6271 Remote Similarity NPC77703
0.626 Remote Similarity NPC287764
0.626 Remote Similarity NPC139778
0.625 Remote Similarity NPC25110
0.625 Remote Similarity NPC135005
0.624 Remote Similarity NPC478137
0.6231 Remote Similarity NPC472458
0.6218 Remote Similarity NPC247060
0.6218 Remote Similarity NPC176012
0.6216 Remote Similarity NPC43308
0.621 Remote Similarity NPC79238
0.6204 Remote Similarity NPC215474
0.6202 Remote Similarity NPC99905
0.6202 Remote Similarity NPC96080
0.6202 Remote Similarity NPC208118
0.6198 Remote Similarity NPC476328
0.619 Remote Similarity NPC145501
0.6167 Remote Similarity NPC98765
0.6148 Remote Similarity NPC46981
0.6129 Remote Similarity NPC63511
0.6121 Remote Similarity NPC155985
0.6119 Remote Similarity NPC476497
0.6116 Remote Similarity NPC476921
0.6116 Remote Similarity NPC212874
0.6106 Remote Similarity NPC323156
0.6102 Remote Similarity NPC91604
0.6091 Remote Similarity NPC175419
0.6047 Remote Similarity NPC475887
0.6045 Remote Similarity NPC476501
0.6036 Remote Similarity NPC75810
0.6032 Remote Similarity NPC476498
0.6031 Remote Similarity NPC238323
0.6031 Remote Similarity NPC476504
0.6029 Remote Similarity NPC478139
0.6017 Remote Similarity NPC474164
0.6016 Remote Similarity NPC169375
0.6015 Remote Similarity NPC321197
0.6 Remote Similarity NPC475340
0.6 Remote Similarity NPC328052
0.6 Remote Similarity NPC323180
0.5982 Remote Similarity NPC321340
0.5982 Remote Similarity NPC119633
0.5982 Remote Similarity NPC171698
0.5982 Remote Similarity NPC270957
0.598 Remote Similarity NPC124384
0.597 Remote Similarity NPC237286
0.5963 Remote Similarity NPC192456
0.5938 Remote Similarity NPC476499
0.5929 Remote Similarity NPC89747
0.5929 Remote Similarity NPC474210
0.5926 Remote Similarity NPC96010
0.5926 Remote Similarity NPC317654
0.5917 Remote Similarity NPC477964
0.5917 Remote Similarity NPC275686
0.5896 Remote Similarity NPC476503
0.5893 Remote Similarity NPC182106
0.5893 Remote Similarity NPC311769
0.5842 Remote Similarity NPC44122
0.584 Remote Similarity NPC476918
0.5839 Remote Similarity NPC476967
0.5833 Remote Similarity NPC42853
0.5833 Remote Similarity NPC477819
0.5833 Remote Similarity NPC477817
0.5825 Remote Similarity NPC245223
0.5825 Remote Similarity NPC477820
0.5818 Remote Similarity NPC257962
0.581 Remote Similarity NPC310766
0.581 Remote Similarity NPC232112
0.58 Remote Similarity NPC281540
0.58 Remote Similarity NPC167995
0.58 Remote Similarity NPC159654
0.58 Remote Similarity NPC118937
0.5794 Remote Similarity NPC253645
0.5794 Remote Similarity NPC95920
0.5794 Remote Similarity NPC85001
0.5794 Remote Similarity NPC147835
0.5794 Remote Similarity NPC218602
0.5789 Remote Similarity NPC473525
0.5784 Remote Similarity NPC63190
0.578 Remote Similarity NPC49627
0.578 Remote Similarity NPC49599
0.578 Remote Similarity NPC1319
0.5776 Remote Similarity NPC126993
0.5772 Remote Similarity NPC90538
0.5772 Remote Similarity NPC473254
0.5769 Remote Similarity NPC304646
0.5769 Remote Similarity NPC63588
0.5769 Remote Similarity NPC28280
0.5769 Remote Similarity NPC476502
0.5769 Remote Similarity NPC251201
0.5769 Remote Similarity NPC232925
0.5766 Remote Similarity NPC212106
0.5766 Remote Similarity NPC477352
0.5763 Remote Similarity NPC111015
0.5752 Remote Similarity NPC76518
0.5752 Remote Similarity NPC22133
0.575 Remote Similarity NPC240650
0.575 Remote Similarity NPC91036
0.575 Remote Similarity NPC184033
0.5741 Remote Similarity NPC260301
0.5741 Remote Similarity NPC138502
0.5741 Remote Similarity NPC307336
0.5739 Remote Similarity NPC259252
0.5736 Remote Similarity NPC28224
0.5727 Remote Similarity NPC71535
0.5727 Remote Similarity NPC78545
0.5726 Remote Similarity NPC272746
0.5726 Remote Similarity NPC110923
0.5726 Remote Similarity NPC119329
0.5726 Remote Similarity NPC74296
0.5725 Remote Similarity NPC309249
0.5725 Remote Similarity NPC39485
0.5725 Remote Similarity NPC221196
0.5714 Remote Similarity NPC151018
0.5714 Remote Similarity NPC156277
0.5714 Remote Similarity NPC245866
0.5714 Remote Similarity NPC320549
0.5714 Remote Similarity NPC58057
0.5714 Remote Similarity NPC110778
0.5714 Remote Similarity NPC246956
0.5714 Remote Similarity NPC477818
0.5714 Remote Similarity NPC472743
0.5714 Remote Similarity NPC111234
0.5714 Remote Similarity NPC475726
0.5702 Remote Similarity NPC72133
0.5702 Remote Similarity NPC98236
0.5702 Remote Similarity NPC322672
0.5702 Remote Similarity NPC471737
0.5702 Remote Similarity NPC269396
0.5702 Remote Similarity NPC323958
0.5701 Remote Similarity NPC125767
0.5701 Remote Similarity NPC212879
0.5701 Remote Similarity NPC195155
0.5701 Remote Similarity NPC240235
0.5701 Remote Similarity NPC70982
0.5701 Remote Similarity NPC185536
0.5701 Remote Similarity NPC174964

  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 NPC470595 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
0.6838 Remote Similarity NPD7646 Clinical (unspecified phase)
0.6803 Remote Similarity NPD7754 Approved
0.6803 Remote Similarity NPD7755 Approved
0.6752 Remote Similarity NPD6920 Discontinued
0.6639 Remote Similarity NPD6415 Discontinued
0.6557 Remote Similarity NPD8077 Approved
0.6557 Remote Similarity NPD8078 Approved
0.6504 Remote Similarity NPD8298 Phase 2
0.6471 Remote Similarity NPD8040 Discontinued
0.6441 Remote Similarity NPD7912 Approved
0.6441 Remote Similarity NPD7911 Approved
0.6441 Remote Similarity NPD7986 Approved
0.6441 Remote Similarity NPD7987 Approved
0.6435 Remote Similarity NPD7919 Phase 3
0.6435 Remote Similarity NPD7920 Phase 3
0.6379 Remote Similarity NPD8088 Phase 1
0.6281 Remote Similarity NPD7990 Approved
0.6281 Remote Similarity NPD7989 Approved
0.6186 Remote Similarity NPD8418 Phase 2
0.6121 Remote Similarity NPD7991 Discontinued
0.6066 Remote Similarity NPD7333 Discontinued
0.6031 Remote Similarity NPD6909 Approved
0.6031 Remote Similarity NPD6908 Approved
0.5984 Remote Similarity NPD1376 Discontinued
0.5982 Remote Similarity NPD8308 Discontinued
0.5926 Remote Similarity NPD7155 Clinical (unspecified phase)
0.5913 Remote Similarity NPD6934 Discontinued
0.5781 Remote Similarity NPD7336 Phase 2
0.5781 Remote Similarity NPD7337 Clinical (unspecified phase)
0.5781 Remote Similarity NPD7335 Phase 2
0.5769 Remote Similarity NPD4245 Approved
0.5769 Remote Similarity NPD4244 Approved
0.5714 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4788 Approved
0.5714 Remote Similarity NPD4808 Clinical (unspecified phase)
0.569 Remote Similarity NPD5328 Approved
0.5678 Remote Similarity NPD4202 Approved
0.5673 Remote Similarity NPD3698 Phase 2
0.5664 Remote Similarity NPD3666 Approved
0.5664 Remote Similarity NPD3665 Phase 1
0.5664 Remote Similarity NPD3133 Approved
0.5648 Remote Similarity NPD6117 Approved
0.5619 Remote Similarity NPD4787 Phase 1
0.5614 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5607 Remote Similarity NPD6113 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