Structure

Physi-Chem Properties

Molecular Weight:  249.14
Volume:  248.569
LogP:  1.777
LogD:  1.349
LogS:  -2.066
# Rotatable Bonds:  1
TPSA:  38.77
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.518
Synthetic Accessibility Score:  5.714
Fsp3:  0.786
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.663
MDCK Permeability:  7.412115519400686e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.348
Human Intestinal Absorption (HIA):  0.037
20% Bioavailability (F20%):  0.036
30% Bioavailability (F30%):  0.905

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.735
Plasma Protein Binding (PPB):  25.344463348388672%
Volume Distribution (VD):  1.533
Pgp-substrate:  75.49518585205078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.027
CYP1A2-substrate:  0.114
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.8
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.074
CYP2D6-inhibitor:  0.064
CYP2D6-substrate:  0.831
CYP3A4-inhibitor:  0.076
CYP3A4-substrate:  0.883

ADMET: Excretion

Clearance (CL):  14.452
Half-life (T1/2):  0.174

ADMET: Toxicity

hERG Blockers:  0.031
Human Hepatotoxicity (H-HT):  0.165
Drug-inuced Liver Injury (DILI):  0.253
AMES Toxicity:  0.781
Rat Oral Acute Toxicity:  0.933
Maximum Recommended Daily Dose:  0.789
Skin Sensitization:  0.667
Carcinogencity:  0.838
Eye Corrosion:  0.091
Eye Irritation:  0.131
Respiratory Toxicity:  0.969

Download Data

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

  Natural Product: NPC44514

Natural Product ID:  NPC44514
Common Name*:   Securinega Amamine C
IUPAC Name:   n.a.
Synonyms:   Securinega Amamine C
Standard InCHIKey:  FTCISLOTUCZXTN-FMSGJZPZSA-N
Standard InCHI:  InChI=1S/C14H19NO3/c1-17-11-6-9-7-13(16)18-14(9)8-10(11)15-5-3-2-4-12(14)15/h7,10-12H,2-6,8H2,1H3/t10-,11-,12+,14-/m0/s1
SMILES:  CO[C@H]1CC2=CC(=O)O[C@]32C[C@@H]1N1CCCC[C@H]31
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL398307
PubChem CID:   24762834
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000251] Indolizidines

*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
NPO19434.1 Securinega suffruticosa Under-species n.a. n.a. n.a. wood n.a. PMID[18052029]

☑ 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
NPT91 Cell Line KB Homo sapiens IC50 > 5.0 ug.mL-1 PMID[561913]
NPT137 Cell Line L1210 Mus musculus IC50 > 5.0 ug.mL-1 PMID[561913]

☑ 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 NPC44514 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
0.9897 High Similarity NPC93179
0.8095 Intermediate Similarity NPC473289
0.7921 Intermediate Similarity NPC110875
0.7921 Intermediate Similarity NPC299808
0.7921 Intermediate Similarity NPC118844
0.7921 Intermediate Similarity NPC72183
0.7615 Intermediate Similarity NPC75523
0.7315 Intermediate Similarity NPC270813
0.7 Intermediate Similarity NPC174463
0.6885 Remote Similarity NPC230849
0.688 Remote Similarity NPC477987
0.688 Remote Similarity NPC329401
0.6842 Remote Similarity NPC477000
0.6842 Remote Similarity NPC477001
0.6723 Remote Similarity NPC43648
0.6667 Remote Similarity NPC477985
0.6667 Remote Similarity NPC477988
0.6667 Remote Similarity NPC326386
0.6667 Remote Similarity NPC471087
0.6667 Remote Similarity NPC138534
0.6667 Remote Similarity NPC477986
0.6609 Remote Similarity NPC173690
0.6609 Remote Similarity NPC80439
0.6609 Remote Similarity NPC6271
0.6609 Remote Similarity NPC279833
0.6581 Remote Similarity NPC271562
0.6552 Remote Similarity NPC64168
0.6552 Remote Similarity NPC133420
0.6529 Remote Similarity NPC193471
0.6529 Remote Similarity NPC130124
0.6512 Remote Similarity NPC471086
0.6512 Remote Similarity NPC478136
0.6504 Remote Similarity NPC469997
0.6504 Remote Similarity NPC65045
0.65 Remote Similarity NPC47857
0.65 Remote Similarity NPC168758
0.65 Remote Similarity NPC58281
0.65 Remote Similarity NPC181510
0.648 Remote Similarity NPC11379
0.6457 Remote Similarity NPC323168
0.6457 Remote Similarity NPC477990
0.6457 Remote Similarity NPC111162
0.6457 Remote Similarity NPC477989
0.6457 Remote Similarity NPC293550
0.6452 Remote Similarity NPC235625
0.6385 Remote Similarity NPC173173
0.6364 Remote Similarity NPC316984
0.6364 Remote Similarity NPC30911
0.6356 Remote Similarity NPC86906
0.6341 Remote Similarity NPC474984
0.632 Remote Similarity NPC284656
0.632 Remote Similarity NPC106791
0.632 Remote Similarity NPC201889
0.6311 Remote Similarity NPC474995
0.6308 Remote Similarity NPC317654
0.6308 Remote Similarity NPC96010
0.6299 Remote Similarity NPC23963
0.6299 Remote Similarity NPC470000
0.6296 Remote Similarity NPC130436
0.6296 Remote Similarity NPC469861
0.6296 Remote Similarity NPC469860
0.629 Remote Similarity NPC28280
0.629 Remote Similarity NPC304646
0.623 Remote Similarity NPC474459
0.6179 Remote Similarity NPC474452
0.6174 Remote Similarity NPC241426
0.6165 Remote Similarity NPC215507
0.6165 Remote Similarity NPC307165
0.6154 Remote Similarity NPC469999
0.6154 Remote Similarity NPC188785
0.6148 Remote Similarity NPC472313
0.614 Remote Similarity NPC150041
0.6111 Remote Similarity NPC96055
0.6098 Remote Similarity NPC79238
0.6078 Remote Similarity NPC470994
0.6074 Remote Similarity NPC133089
0.6071 Remote Similarity NPC159568
0.6061 Remote Similarity NPC476951
0.6047 Remote Similarity NPC476504
0.6034 Remote Similarity NPC476344
0.6031 Remote Similarity NPC26285
0.6016 Remote Similarity NPC471261
0.6016 Remote Similarity NPC113012
0.6016 Remote Similarity NPC122926
0.6 Remote Similarity NPC281104
0.6 Remote Similarity NPC120335
0.6 Remote Similarity NPC475988
0.596 Remote Similarity NPC472266
0.595 Remote Similarity NPC101106
0.595 Remote Similarity NPC135216
0.5942 Remote Similarity NPC82129
0.5935 Remote Similarity NPC474891
0.5926 Remote Similarity NPC471218
0.592 Remote Similarity NPC80834
0.592 Remote Similarity NPC469968
0.5909 Remote Similarity NPC476503
0.5906 Remote Similarity NPC470538
0.5905 Remote Similarity NPC189206
0.5902 Remote Similarity NPC250187
0.5902 Remote Similarity NPC46981
0.59 Remote Similarity NPC276290
0.5897 Remote Similarity NPC4834
0.5882 Remote Similarity NPC314792
0.5882 Remote Similarity NPC474348
0.5868 Remote Similarity NPC469604
0.5868 Remote Similarity NPC212874
0.5854 Remote Similarity NPC287572
0.5854 Remote Similarity NPC470535
0.5854 Remote Similarity NPC471636
0.5854 Remote Similarity NPC474969
0.5854 Remote Similarity NPC476034
0.5852 Remote Similarity NPC470539
0.5849 Remote Similarity NPC184737
0.584 Remote Similarity NPC469455
0.5833 Remote Similarity NPC474244
0.5814 Remote Similarity NPC9714
0.5814 Remote Similarity NPC476952
0.5806 Remote Similarity NPC470536
0.5806 Remote Similarity NPC218602
0.58 Remote Similarity NPC475342
0.5798 Remote Similarity NPC474985
0.5797 Remote Similarity NPC120420
0.5794 Remote Similarity NPC295444
0.5794 Remote Similarity NPC268327
0.5794 Remote Similarity NPC273215
0.5794 Remote Similarity NPC279383
0.5789 Remote Similarity NPC321197
0.5785 Remote Similarity NPC265094
0.5781 Remote Similarity NPC288629
0.5772 Remote Similarity NPC313272
0.5772 Remote Similarity NPC319537
0.5772 Remote Similarity NPC176773
0.5766 Remote Similarity NPC261730
0.5763 Remote Similarity NPC52820
0.576 Remote Similarity NPC127578
0.5758 Remote Similarity NPC478138
0.5755 Remote Similarity NPC187568
0.5755 Remote Similarity NPC41780
0.5755 Remote Similarity NPC99864
0.5752 Remote Similarity NPC93411
0.575 Remote Similarity NPC474873
0.5748 Remote Similarity NPC478137
0.5746 Remote Similarity NPC309525
0.5741 Remote Similarity NPC268827
0.5738 Remote Similarity NPC87919
0.5736 Remote Similarity NPC147707
0.5727 Remote Similarity NPC170286
0.5726 Remote Similarity NPC119225
0.5726 Remote Similarity NPC476261
0.5726 Remote Similarity NPC25033
0.5726 Remote Similarity NPC470382
0.5726 Remote Similarity NPC471635
0.5714 Remote Similarity NPC29501
0.5714 Remote Similarity NPC297058
0.5714 Remote Similarity NPC91604
0.5714 Remote Similarity NPC147238
0.5714 Remote Similarity NPC315170
0.5704 Remote Similarity NPC280903
0.5701 Remote Similarity NPC299235
0.5693 Remote Similarity NPC478139
0.5692 Remote Similarity NPC471673
0.569 Remote Similarity NPC7349
0.5686 Remote Similarity NPC232812
0.5682 Remote Similarity NPC242692
0.5682 Remote Similarity NPC315188
0.5678 Remote Similarity NPC194132
0.5678 Remote Similarity NPC476449
0.5676 Remote Similarity NPC30486
0.5676 Remote Similarity NPC475975
0.5673 Remote Similarity NPC16349
0.5673 Remote Similarity NPC222244
0.5669 Remote Similarity NPC476498
0.5669 Remote Similarity NPC478024
0.5669 Remote Similarity NPC269340
0.5662 Remote Similarity NPC474847
0.566 Remote Similarity NPC123360
0.5659 Remote Similarity NPC30196
0.5656 Remote Similarity NPC473254
0.5656 Remote Similarity NPC469895
0.5652 Remote Similarity NPC316401
0.5648 Remote Similarity NPC471768
0.5643 Remote Similarity NPC239252
0.5643 Remote Similarity NPC471256
0.5643 Remote Similarity NPC473703
0.5641 Remote Similarity NPC140277
0.5641 Remote Similarity NPC105490
0.5639 Remote Similarity NPC472458
0.5639 Remote Similarity NPC20035
0.5636 Remote Similarity NPC178676
0.5636 Remote Similarity NPC173609
0.5635 Remote Similarity NPC63511
0.5635 Remote Similarity NPC469603
0.5631 Remote Similarity NPC37929
0.5631 Remote Similarity NPC469660
0.5631 Remote Similarity NPC64234
0.5625 Remote Similarity NPC75810
0.5625 Remote Similarity NPC474013
0.5625 Remote Similarity NPC319991
0.5625 Remote Similarity NPC471795
0.562 Remote Similarity NPC144714

  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 NPC44514 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
0.6364 Remote Similarity NPD2204 Approved
0.6354 Remote Similarity NPD616 Clinical (unspecified phase)
0.6228 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6 Remote Similarity NPD2569 Approved
0.6 Remote Similarity NPD2567 Approved
0.595 Remote Similarity NPD4211 Phase 1
0.5906 Remote Similarity NPD7755 Approved
0.5906 Remote Similarity NPD7754 Approved
0.5873 Remote Similarity NPD1376 Discontinued
0.5794 Remote Similarity NPD4572 Approved
0.5794 Remote Similarity NPD4573 Approved
0.5794 Remote Similarity NPD4571 Approved
0.5772 Remote Similarity NPD812 Approved
0.5772 Remote Similarity NPD811 Approved
0.5772 Remote Similarity NPD810 Approved
0.5758 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5755 Remote Similarity NPD8415 Approved
0.5714 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2201 Approved
0.5686 Remote Similarity NPD2697 Approved
0.5686 Remote Similarity NPD2696 Approved
0.5686 Remote Similarity NPD2694 Approved
0.5686 Remote Similarity NPD2695 Approved
0.5669 Remote Similarity NPD8078 Approved
0.5669 Remote Similarity NPD8077 Approved
0.5656 Remote Similarity NPD2258 Approved
0.5656 Remote Similarity NPD2259 Approved
0.5643 Remote Similarity NPD4621 Approved
0.5643 Remote Similarity NPD4619 Approved
0.563 Remote Similarity NPD8451 Approved
0.5612 Remote Similarity NPD2613 Approved
0.5603 Remote Similarity NPD3614 Approved
0.5603 Remote Similarity NPD2574 Discontinued
0.5603 Remote Similarity NPD2573 Approved
0.5603 Remote Similarity NPD3090 Approved
0.5603 Remote Similarity NPD3089 Approved
0.5603 Remote Similarity NPD2566 Approved
0.5603 Remote Similarity NPD3616 Approved
0.5603 Remote Similarity NPD4746 Phase 3
0.5603 Remote Similarity NPD4745 Approved
0.5603 Remote Similarity NPD3087 Approved
0.5603 Remote Similarity NPD3615 Approved
0.5603 Remote Similarity NPD3088 Approved
0.5603 Remote Similarity NPD2571 Approved
0.5603 Remote Similarity NPD2572 Clinical (unspecified phase)
0.5603 Remote Similarity NPD2570 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