Structure

Physi-Chem Properties

Molecular Weight:  217.11
Volume:  219.846
LogP:  1.893
LogD:  1.179
LogS:  -1.978
# Rotatable Bonds:  0
TPSA:  29.54
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.574
Synthetic Accessibility Score:  5.56
Fsp3:  0.615
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:  -4.715
MDCK Permeability:  2.7869085897691548e-05
Pgp-inhibitor:  0.062
Pgp-substrate:  0.107
Human Intestinal Absorption (HIA):  0.22
20% Bioavailability (F20%):  0.988
30% Bioavailability (F30%):  0.622

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.994
Plasma Protein Binding (PPB):  51.26678466796875%
Volume Distribution (VD):  1.76
Pgp-substrate:  54.10651397705078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.03
CYP1A2-substrate:  0.543
CYP2C19-inhibitor:  0.216
CYP2C19-substrate:  0.856
CYP2C9-inhibitor:  0.083
CYP2C9-substrate:  0.551
CYP2D6-inhibitor:  0.227
CYP2D6-substrate:  0.874
CYP3A4-inhibitor:  0.129
CYP3A4-substrate:  0.874

ADMET: Excretion

Clearance (CL):  10.443
Half-life (T1/2):  0.63

ADMET: Toxicity

hERG Blockers:  0.073
Human Hepatotoxicity (H-HT):  0.63
Drug-inuced Liver Injury (DILI):  0.056
AMES Toxicity:  0.395
Rat Oral Acute Toxicity:  0.906
Maximum Recommended Daily Dose:  0.962
Skin Sensitization:  0.953
Carcinogencity:  0.749
Eye Corrosion:  0.004
Eye Irritation:  0.016
Respiratory Toxicity:  0.714

Download Data

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

  Natural Product: NPC118844

Natural Product ID:  NPC118844
Common Name*:   SWZMSZQQJRKFBP-KKPNGEORSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SWZMSZQQJRKFBP-KKPNGEORSA-N
Standard InCHI:  InChI=1S/C13H15NO2/c15-12-7-9-4-5-10-8-13(9,16-12)11-3-1-2-6-14(10)11/h4-5,7,10-11H,1-3,6,8H2/t10-,11-,13?/m1/s1
SMILES:  O=C1C=C2C3(O1)C[C@@H](C=C2)N1[C@@H]3CCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1529147
PubChem CID:   6338099
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
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[12628396]
NPO19434 Securinega suffruticosa Species Phyllanthaceae Eukaryota n.a. callus n.a. PMID[16327202]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota Hairy roots n.a. n.a. PMID[19271765]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[26285573]
NPO19434 Securinega suffruticosa Species Phyllanthaceae Eukaryota Twigs n.a. n.a. PMID[31082231]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6619887]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6631435]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264679]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264682]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7320741]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19434 Securinega suffruticosa Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17106 Phyllanthus discoides Species Leiothrichidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19434 Securinega suffruticosa Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17106 Phyllanthus discoides Species Leiothrichidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17106 Phyllanthus discoides Species Leiothrichidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19434 Securinega suffruticosa Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17106 Phyllanthus discoides Species Leiothrichidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19434 Securinega suffruticosa Species Phyllanthaceae 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
NPT3 Individual Protein Thioredoxin glutathione reductase Schistosoma mansoni Potency = 50118.7 nM PMID[447938]
NPT56 Individual Protein Beta-lactamase AmpC Escherichia coli K-12 Potency = 5623.4 nM PMID[447938]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 580.5 nM PMID[447938]
NPT64 Individual Protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 3661.1 nM PMID[447938]
NPT5 Individual Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens Potency n.a. 8912.5 nM PMID[447938]
NPT64 Individual Protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 35481.3 nM PMID[447938]
NPT154 Individual Protein Mothers against decapentaplegic homolog 3 Homo sapiens Potency n.a. 6309.6 nM PMID[447938]
NPT477 Individual Protein DNA dC->dU-editing enzyme APOBEC-3G Homo sapiens Potency n.a. 35481.3 nM PMID[447938]
NPT100 Individual Protein Glutaminase kidney isoform, mitochondrial Homo sapiens Potency n.a. 8912.5 nM PMID[447938]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 501.2 nM PMID[447938]
NPT478 Individual Protein Ataxin-2 Homo sapiens Potency n.a. 19952.6 nM PMID[447938]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 17782.8 nM PMID[447938]
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency n.a. 18356.4 nM PMID[447938]
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency n.a. 29092.9 nM PMID[447938]
NPT2 Others Unspecified CC50 = 39402.0 nM PMID[447938]
NPT2 Others Unspecified IC90 > 100000.0 nM PMID[447938]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 11689.1 nM PMID[447938]
NPT2 Others Unspecified Potency n.a. 5011.9 nM PMID[447938]
NPT2 Others Unspecified Potency n.a. 25118.9 nM PMID[447938]
NPT2 Others Unspecified Potency n.a. 14581.0 nM PMID[447938]
NPT2 Others Unspecified Potency n.a. 11220.2 nM PMID[447938]
NPT2 Others Unspecified Potency n.a. 39810.7 nM PMID[447938]

☑ 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 NPC118844 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 NPC299808
1.0 High Similarity NPC110875
1.0 High Similarity NPC72183
0.9043 High Similarity NPC473289
0.8144 Intermediate Similarity NPC270813
0.7921 Intermediate Similarity NPC75523
0.7921 Intermediate Similarity NPC44514
0.7843 Intermediate Similarity NPC93179
0.6916 Remote Similarity NPC133420
0.6837 Remote Similarity NPC469860
0.6837 Remote Similarity NPC469861
0.6837 Remote Similarity NPC130436
0.6807 Remote Similarity NPC477987
0.6807 Remote Similarity NPC329401
0.6667 Remote Similarity NPC241426
0.6637 Remote Similarity NPC43648
0.663 Remote Similarity NPC470994
0.6606 Remote Similarity NPC469604
0.6585 Remote Similarity NPC477988
0.6514 Remote Similarity NPC173690
0.6514 Remote Similarity NPC80439
0.6514 Remote Similarity NPC279833
0.6514 Remote Similarity NPC6271
0.6455 Remote Similarity NPC477000
0.6455 Remote Similarity NPC64168
0.6455 Remote Similarity NPC477001
0.6435 Remote Similarity NPC130124
0.6435 Remote Similarity NPC193471
0.641 Remote Similarity NPC469997
0.641 Remote Similarity NPC65045
0.6404 Remote Similarity NPC168758
0.6404 Remote Similarity NPC181510
0.6404 Remote Similarity NPC47857
0.6316 Remote Similarity NPC469603
0.6303 Remote Similarity NPC477986
0.6303 Remote Similarity NPC138534
0.6273 Remote Similarity NPC474244
0.6261 Remote Similarity NPC316984
0.6261 Remote Similarity NPC30911
0.625 Remote Similarity NPC230849
0.6239 Remote Similarity NPC474984
0.6218 Remote Similarity NPC201889
0.6218 Remote Similarity NPC284656
0.6218 Remote Similarity NPC106791
0.6218 Remote Similarity NPC174463
0.6207 Remote Similarity NPC474995
0.6204 Remote Similarity NPC52820
0.6198 Remote Similarity NPC470000
0.616 Remote Similarity NPC478136
0.6121 Remote Similarity NPC58281
0.6098 Remote Similarity NPC111162
0.6098 Remote Similarity NPC293550
0.6098 Remote Similarity NPC323168
0.6098 Remote Similarity NPC477990
0.6098 Remote Similarity NPC477989
0.6066 Remote Similarity NPC23963
0.6053 Remote Similarity NPC271562
0.6048 Remote Similarity NPC469999
0.6048 Remote Similarity NPC26285
0.6038 Remote Similarity NPC145707
0.6022 Remote Similarity NPC232812
0.6 Remote Similarity NPC471636
0.6 Remote Similarity NPC287572
0.6 Remote Similarity NPC474099
0.5984 Remote Similarity NPC11379
0.5965 Remote Similarity NPC86906
0.596 Remote Similarity NPC471768
0.5957 Remote Similarity NPC64234
0.5957 Remote Similarity NPC37929
0.5952 Remote Similarity NPC96010
0.5952 Remote Similarity NPC317654
0.595 Remote Similarity NPC235625
0.5946 Remote Similarity NPC26597
0.5934 Remote Similarity NPC182794
0.5929 Remote Similarity NPC199831
0.5929 Remote Similarity NPC474828
0.5929 Remote Similarity NPC474827
0.5929 Remote Similarity NPC68001
0.5922 Remote Similarity NPC76283
0.592 Remote Similarity NPC471087
0.592 Remote Similarity NPC326386
0.592 Remote Similarity NPC477985
0.5918 Remote Similarity NPC54996
0.5917 Remote Similarity NPC288629
0.5917 Remote Similarity NPC304646
0.5917 Remote Similarity NPC28280
0.5909 Remote Similarity NPC476344
0.5909 Remote Similarity NPC4834
0.5906 Remote Similarity NPC173173
0.59 Remote Similarity NPC268827
0.5897 Remote Similarity NPC63511
0.5897 Remote Similarity NPC113012
0.5897 Remote Similarity NPC122926
0.5893 Remote Similarity NPC314792
0.5891 Remote Similarity NPC120335
0.5882 Remote Similarity NPC475988
0.5872 Remote Similarity NPC150041
0.587 Remote Similarity NPC191233
0.5851 Remote Similarity NPC265574
0.5826 Remote Similarity NPC472433
0.5826 Remote Similarity NPC101106
0.5826 Remote Similarity NPC135216
0.5825 Remote Similarity NPC475975
0.582 Remote Similarity NPC471673
0.5818 Remote Similarity NPC476449
0.5812 Remote Similarity NPC474891
0.5806 Remote Similarity NPC21998
0.5804 Remote Similarity NPC474985
0.5798 Remote Similarity NPC269340
0.5798 Remote Similarity NPC474452
0.5781 Remote Similarity NPC471086
0.5776 Remote Similarity NPC250187
0.5769 Remote Similarity NPC296589
0.5763 Remote Similarity NPC472313
0.5761 Remote Similarity NPC220766
0.5752 Remote Similarity NPC144714
0.5752 Remote Similarity NPC188785
0.5752 Remote Similarity NPC100810
0.5745 Remote Similarity NPC276290
0.5743 Remote Similarity NPC476560
0.573 Remote Similarity NPC133600
0.5726 Remote Similarity NPC476034
0.5726 Remote Similarity NPC474969
0.5714 Remote Similarity NPC29501
0.5714 Remote Similarity NPC474459
0.5714 Remote Similarity NPC79238
0.5703 Remote Similarity NPC476951
0.5699 Remote Similarity NPC116013
0.5694 Remote Similarity NPC475342
0.5692 Remote Similarity NPC215507
0.5688 Remote Similarity NPC1108
0.5684 Remote Similarity NPC470693
0.5676 Remote Similarity NPC175614
0.5676 Remote Similarity NPC474129
0.567 Remote Similarity NPC252503
0.567 Remote Similarity NPC222244
0.567 Remote Similarity NPC16349
0.5667 Remote Similarity NPC295444
0.5667 Remote Similarity NPC279383
0.5667 Remote Similarity NPC314550
0.5667 Remote Similarity NPC273215
0.5667 Remote Similarity NPC429928
0.5667 Remote Similarity NPC268327
0.5662 Remote Similarity NPC281104
0.5656 Remote Similarity NPC477554
0.5648 Remote Similarity NPC47230
0.5648 Remote Similarity NPC159568
0.5648 Remote Similarity NPC17143
0.5638 Remote Similarity NPC472266
0.5636 Remote Similarity NPC313265
0.563 Remote Similarity NPC127578
0.5625 Remote Similarity NPC316029
0.5625 Remote Similarity NPC91036
0.5615 Remote Similarity NPC470539
0.5614 Remote Similarity NPC474873
0.561 Remote Similarity NPC477553
0.5603 Remote Similarity NPC205176
0.56 Remote Similarity NPC473825
0.56 Remote Similarity NPC187568
0.56 Remote Similarity NPC41780

  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 NPC118844 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
0.6261 Remote Similarity NPD2204 Approved
0.6222 Remote Similarity NPD616 Clinical (unspecified phase)
0.6121 Remote Similarity NPD2201 Approved
0.6111 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5826 Remote Similarity NPD4211 Phase 1
0.5798 Remote Similarity NPD4573 Approved
0.5798 Remote Similarity NPD4572 Approved
0.5798 Remote Similarity NPD4571 Approved
0.5776 Remote Similarity NPD812 Approved
0.5776 Remote Similarity NPD810 Approved
0.5776 Remote Similarity NPD811 Approved
0.5763 Remote Similarity NPD5239 Approved
0.5763 Remote Similarity NPD5237 Approved
0.5763 Remote Similarity NPD5236 Approved
0.5763 Remote Similarity NPD5235 Approved
0.5763 Remote Similarity NPD5240 Approved
0.5662 Remote Similarity NPD2569 Approved
0.5662 Remote Similarity NPD2567 Approved
0.5625 Remote Similarity NPD8451 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