Structure

Physi-Chem Properties

Molecular Weight:  279.15
Volume:  274.655
LogP:  0.937
LogD:  0.932
LogS:  -1.738
# Rotatable Bonds:  2
TPSA:  48.0
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.702
Synthetic Accessibility Score:  5.871
Fsp3:  0.8
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:  -4.599
MDCK Permeability:  6.124736682977527e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.191
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.631
30% Bioavailability (F30%):  0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.353
Plasma Protein Binding (PPB):  14.543943405151367%
Volume Distribution (VD):  1.536
Pgp-substrate:  81.21062469482422%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.111
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.875
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.034
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.647
CYP3A4-inhibitor:  0.026
CYP3A4-substrate:  0.919

ADMET: Excretion

Clearance (CL):  11.063
Half-life (T1/2):  0.208

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.797
Drug-inuced Liver Injury (DILI):  0.04
AMES Toxicity:  0.435
Rat Oral Acute Toxicity:  0.615
Maximum Recommended Daily Dose:  0.962
Skin Sensitization:  0.944
Carcinogencity:  0.87
Eye Corrosion:  0.073
Eye Irritation:  0.075
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: NPC93179

Natural Product ID:  NPC93179
Common Name*:   Securinega Amamine B
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KBEIBRVSMQBGPK-CXOVXGEYSA-N
Standard InCHI:  InChI=1S/C15H21NO4/c1-18-10-3-4-16-11-8-15(13(16)7-10)9(5-12(11)19-2)6-14(17)20-15/h6,10-13H,3-5,7-8H2,1-2H3/t10-,11-,12-,13-,15-/m0/s1
SMILES:  CO[C@H]1CCN2[C@@H](C1)[C@]13OC(=O)C=C3C[C@@H]([C@@H]2C1)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL251668
PubChem CID:   24762833
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[517656]
NPT137 Cell Line L1210 Mus musculus IC50 > 5.0 ug.mL-1 PMID[517656]

☑ 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 NPC93179 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 NPC44514
0.8019 Intermediate Similarity NPC473289
0.7843 Intermediate Similarity NPC118844
0.7843 Intermediate Similarity NPC110875
0.7843 Intermediate Similarity NPC72183
0.7843 Intermediate Similarity NPC299808
0.7706 Intermediate Similarity NPC75523
0.7248 Intermediate Similarity NPC270813
0.7083 Intermediate Similarity NPC174463
0.6967 Remote Similarity NPC230849
0.696 Remote Similarity NPC329401
0.696 Remote Similarity NPC477987
0.6807 Remote Similarity NPC43648
0.6783 Remote Similarity NPC477001
0.6783 Remote Similarity NPC477000
0.6748 Remote Similarity NPC138534
0.6748 Remote Similarity NPC477986
0.6746 Remote Similarity NPC326386
0.6746 Remote Similarity NPC477985
0.6746 Remote Similarity NPC471087
0.6744 Remote Similarity NPC477988
0.6696 Remote Similarity NPC173690
0.6696 Remote Similarity NPC80439
0.6696 Remote Similarity NPC6271
0.6696 Remote Similarity NPC279833
0.6667 Remote Similarity NPC271562
0.6638 Remote Similarity NPC64168
0.6612 Remote Similarity NPC193471
0.6612 Remote Similarity NPC130124
0.6589 Remote Similarity NPC471086
0.6589 Remote Similarity NPC478136
0.6585 Remote Similarity NPC469997
0.6585 Remote Similarity NPC65045
0.6583 Remote Similarity NPC168758
0.6583 Remote Similarity NPC58281
0.6583 Remote Similarity NPC47857
0.6583 Remote Similarity NPC181510
0.656 Remote Similarity NPC11379
0.6535 Remote Similarity NPC323168
0.6535 Remote Similarity NPC111162
0.6535 Remote Similarity NPC293550
0.6535 Remote Similarity NPC477989
0.6535 Remote Similarity NPC477990
0.6532 Remote Similarity NPC235625
0.6496 Remote Similarity NPC133420
0.6462 Remote Similarity NPC173173
0.6446 Remote Similarity NPC30911
0.6446 Remote Similarity NPC316984
0.6423 Remote Similarity NPC474984
0.64 Remote Similarity NPC106791
0.64 Remote Similarity NPC284656
0.64 Remote Similarity NPC201889
0.6393 Remote Similarity NPC474995
0.6389 Remote Similarity NPC130436
0.6389 Remote Similarity NPC469860
0.6389 Remote Similarity NPC469861
0.6378 Remote Similarity NPC23963
0.6378 Remote Similarity NPC470000
0.6303 Remote Similarity NPC86906
0.626 Remote Similarity NPC317654
0.626 Remote Similarity NPC96010
0.6241 Remote Similarity NPC307165
0.6241 Remote Similarity NPC215507
0.624 Remote Similarity NPC28280
0.624 Remote Similarity NPC304646
0.6239 Remote Similarity NPC188785
0.6231 Remote Similarity NPC469999
0.6228 Remote Similarity NPC150041
0.6179 Remote Similarity NPC474459
0.6148 Remote Similarity NPC133089
0.6136 Remote Similarity NPC476951
0.6129 Remote Similarity NPC474452
0.6124 Remote Similarity NPC476504
0.6121 Remote Similarity NPC241426
0.6121 Remote Similarity NPC476344
0.6098 Remote Similarity NPC113012
0.6098 Remote Similarity NPC122926
0.6098 Remote Similarity NPC472313
0.6094 Remote Similarity NPC471261
0.608 Remote Similarity NPC475988
0.6074 Remote Similarity NPC120335
0.6071 Remote Similarity NPC281104
0.6055 Remote Similarity NPC96055
0.6048 Remote Similarity NPC79238
0.6033 Remote Similarity NPC135216
0.6033 Remote Similarity NPC101106
0.6019 Remote Similarity NPC471218
0.6019 Remote Similarity NPC470994
0.6018 Remote Similarity NPC159568
0.6016 Remote Similarity NPC474891
0.6014 Remote Similarity NPC82129
0.5985 Remote Similarity NPC476503
0.5985 Remote Similarity NPC26285
0.5984 Remote Similarity NPC470538
0.5984 Remote Similarity NPC250187
0.595 Remote Similarity NPC469604
0.5935 Remote Similarity NPC476034
0.5935 Remote Similarity NPC287572
0.5935 Remote Similarity NPC471636
0.5935 Remote Similarity NPC474969
0.5935 Remote Similarity NPC470535
0.5926 Remote Similarity NPC470539
0.592 Remote Similarity NPC469455
0.5917 Remote Similarity NPC474244
0.59 Remote Similarity NPC472266
0.5891 Remote Similarity NPC476952
0.5891 Remote Similarity NPC9714
0.5887 Remote Similarity NPC218602
0.5887 Remote Similarity NPC470536
0.5882 Remote Similarity NPC474985
0.5873 Remote Similarity NPC469968
0.5873 Remote Similarity NPC295444
0.5873 Remote Similarity NPC80834
0.5873 Remote Similarity NPC268327
0.5873 Remote Similarity NPC279383
0.5873 Remote Similarity NPC273215
0.587 Remote Similarity NPC120420
0.5868 Remote Similarity NPC265094
0.5867 Remote Similarity NPC475342
0.5865 Remote Similarity NPC321197
0.5854 Remote Similarity NPC319537
0.5854 Remote Similarity NPC313272
0.5854 Remote Similarity NPC46981
0.5849 Remote Similarity NPC189206
0.5847 Remote Similarity NPC4834
0.5847 Remote Similarity NPC52820
0.5842 Remote Similarity NPC276290
0.5841 Remote Similarity NPC93411
0.584 Remote Similarity NPC127578
0.5839 Remote Similarity NPC261730
0.5833 Remote Similarity NPC474873
0.5833 Remote Similarity NPC474348
0.5833 Remote Similarity NPC314792
0.5827 Remote Similarity NPC99864
0.5827 Remote Similarity NPC478137
0.5821 Remote Similarity NPC309525
0.582 Remote Similarity NPC212874
0.5818 Remote Similarity NPC170286
0.5814 Remote Similarity NPC147707
0.5798 Remote Similarity NPC315170
0.5794 Remote Similarity NPC29501
0.5794 Remote Similarity NPC184737
0.5794 Remote Similarity NPC147238
0.5786 Remote Similarity NPC297058
0.5778 Remote Similarity NPC280903
0.5776 Remote Similarity NPC7349
0.5769 Remote Similarity NPC471673
0.5769 Remote Similarity NPC222244
0.5769 Remote Similarity NPC16349
0.5766 Remote Similarity NPC478139
0.5763 Remote Similarity NPC194132
0.5758 Remote Similarity NPC242692
0.5758 Remote Similarity NPC315188
0.5755 Remote Similarity NPC123360
0.5748 Remote Similarity NPC478024
0.5738 Remote Similarity NPC469895
0.5736 Remote Similarity NPC30196
0.5736 Remote Similarity NPC288629
0.5735 Remote Similarity NPC474847
0.5728 Remote Similarity NPC469660
0.5727 Remote Similarity NPC173609
0.5726 Remote Similarity NPC140277
0.5726 Remote Similarity NPC176773
0.5726 Remote Similarity NPC105490
0.5725 Remote Similarity NPC316401
0.5714 Remote Similarity NPC472458
0.5714 Remote Similarity NPC239252
0.5714 Remote Similarity NPC469603
0.5714 Remote Similarity NPC474013
0.5714 Remote Similarity NPC478138
0.5714 Remote Similarity NPC20035
0.5714 Remote Similarity NPC473703
0.5714 Remote Similarity NPC471256
0.5702 Remote Similarity NPC226863
0.5701 Remote Similarity NPC471225
0.5701 Remote Similarity NPC187568
0.5701 Remote Similarity NPC41780
0.5693 Remote Similarity NPC97861
0.5692 Remote Similarity NPC6531
0.5691 Remote Similarity NPC87919
0.5691 Remote Similarity NPC205176
0.5688 Remote Similarity NPC268827
0.5683 Remote Similarity NPC69496
0.5682 Remote Similarity NPC88190
0.568 Remote Similarity NPC474099
0.5678 Remote Similarity NPC470382
0.5678 Remote Similarity NPC471635
0.5678 Remote Similarity NPC119225
0.5678 Remote Similarity NPC476261
0.5678 Remote Similarity NPC25033
0.5678 Remote Similarity NPC276110
0.5676 Remote Similarity NPC12283
0.5676 Remote Similarity NPC474193
0.5676 Remote Similarity NPC474809
0.5674 Remote Similarity NPC245836
0.5674 Remote Similarity NPC233910
0.5672 Remote Similarity NPC318445
0.5672 Remote Similarity NPC316133
0.5669 Remote Similarity NPC476875
0.5667 Remote Similarity NPC91604

  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 NPC93179 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
0.6446 Remote Similarity NPD2204 Approved
0.6289 Remote Similarity NPD616 Clinical (unspecified phase)
0.6174 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6071 Remote Similarity NPD2569 Approved
0.6071 Remote Similarity NPD2567 Approved
0.6033 Remote Similarity NPD4211 Phase 1
0.5984 Remote Similarity NPD7755 Approved
0.5984 Remote Similarity NPD7754 Approved
0.5952 Remote Similarity NPD1376 Discontinued
0.5827 Remote Similarity NPD8415 Approved
0.5786 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5748 Remote Similarity NPD8078 Approved
0.5748 Remote Similarity NPD4571 Approved
0.5748 Remote Similarity NPD8077 Approved
0.5748 Remote Similarity NPD4572 Approved
0.5748 Remote Similarity NPD4573 Approved
0.5738 Remote Similarity NPD2259 Approved
0.5738 Remote Similarity NPD2258 Approved
0.5726 Remote Similarity NPD810 Approved
0.5726 Remote Similarity NPD811 Approved
0.5726 Remote Similarity NPD812 Approved
0.5704 Remote Similarity NPD8451 Approved
0.57 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5683 Remote Similarity NPD2613 Approved
0.5674 Remote Similarity NPD2574 Discontinued
0.5674 Remote Similarity NPD3615 Approved
0.5674 Remote Similarity NPD3087 Approved
0.5674 Remote Similarity NPD4745 Approved
0.5674 Remote Similarity NPD3088 Approved
0.5674 Remote Similarity NPD2571 Approved
0.5674 Remote Similarity NPD2573 Approved
0.5674 Remote Similarity NPD2572 Clinical (unspecified phase)
0.5674 Remote Similarity NPD3614 Approved
0.5674 Remote Similarity NPD3089 Approved
0.5674 Remote Similarity NPD3616 Approved
0.5674 Remote Similarity NPD2566 Approved
0.5674 Remote Similarity NPD3090 Approved
0.5674 Remote Similarity NPD2570 Approved
0.5674 Remote Similarity NPD4746 Phase 3
0.5672 Remote Similarity NPD7642 Approved
0.5669 Remote Similarity NPD2201 Approved
0.5662 Remote Similarity NPD8448 Approved
0.5631 Remote Similarity NPD2696 Approved
0.5631 Remote Similarity NPD2697 Approved
0.5631 Remote Similarity NPD2695 Approved
0.5631 Remote Similarity NPD2694 Approved
0.5608 Remote Similarity NPD2575 Approved
0.5603 Remote Similarity NPD4621 Approved
0.5603 Remote Similarity NPD4619 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