Structure

Physi-Chem Properties

Molecular Weight:  71.07
Volume:  80.181
LogP:  0.257
LogD:  -0.353
LogS:  0.918
# Rotatable Bonds:  0
TPSA:  12.03
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.435
Synthetic Accessibility Score:  2.192
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.607
MDCK Permeability:  6.582644346053712e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.597
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.122

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.894
Plasma Protein Binding (PPB):  13.514286041259766%
Volume Distribution (VD):  1.764
Pgp-substrate:  87.73818969726562%

ADMET: Metabolism

CYP1A2-inhibitor:  0.048
CYP1A2-substrate:  0.116
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.842
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.121
CYP2D6-inhibitor:  0.023
CYP2D6-substrate:  0.843
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.286

ADMET: Excretion

Clearance (CL):  8.877
Half-life (T1/2):  0.513

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.132
Drug-inuced Liver Injury (DILI):  0.052
AMES Toxicity:  0.089
Rat Oral Acute Toxicity:  0.894
Maximum Recommended Daily Dose:  0.049
Skin Sensitization:  0.916
Carcinogencity:  0.067
Eye Corrosion:  0.974
Eye Irritation:  0.971
Respiratory Toxicity:  0.933

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  Natural Product: NPC232311

Natural Product ID:  NPC232311
Common Name*:   Pyrrolidine
IUPAC Name:   pyrrolidine
Synonyms:   Pyrrolidine
Standard InCHIKey:  RWRDLPDLKQPQOW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2
SMILES:  C1CCCN1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL22830
PubChem CID:   31268
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines

*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
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. DOI[10.1016/0045-6535(91)90110-Y]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.foodchem.2013.08.121]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. DOI[10.1021/jf00055a023]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. seed n.a. PMID[11539687]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. PMID[12713418]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Flowers n.a. n.a. PMID[16180814]
NPO8258 Camellia sinensis Species Theaceae Eukaryota seeds Shizuoka prefecture, Japan n.a. PMID[16499314]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[18068204]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. PMID[21080643]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[21434603]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. husk n.a. PMID[21574561]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. leaf n.a. PMID[21574561]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. exocarp n.a. PMID[21800857]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21800857]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. root n.a. PMID[21800857]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. flower n.a. PMID[21922925]
NPO8258 Camellia sinensis Species Theaceae Eukaryota flower buds n.a. n.a. PMID[21925888]
NPO8258 Camellia sinensis Species Theaceae Eukaryota leaves n.a. n.a. PMID[22377672]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. leaf n.a. PMID[23265489]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. seed n.a. PMID[23292602]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaves Bandung, West Java, Indonesia PMID[23621359]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. PMID[29762032]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. pollen n.a. PMID[8987503]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Seed Oil n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Silk Essent. Oil n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Silk Stigma Style n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Pollen Or Spore n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Cob n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Husk Essent. Oil n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Roots n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota Seed Essent. Oil n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO163.1 Daucus carota var. sativa Varieties Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO163.1 Daucus carota var. sativa Varieties Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15810 Zea mays Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8258 Camellia sinensis Species Theaceae 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
NPO20553 NPC232311 Raw Plant 786.5 154 1419 mg/100g Database [DUKE]
NPO15810 NPC232311 Raw Seed 5000 4500 5500 mg/100g Database [DUKE]

☑ 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
NPT1006 Individual Protein Proton-coupled amino acid transporter 1 Homo sapiens Ki = 38000000.0 nM PMID[478548]
NPT1006 Individual Protein Proton-coupled amino acid transporter 1 Homo sapiens pKi = -1.58 mM PMID[478548]
NPT413 Protein Complex Neuronal acetylcholine receptor Rattus norvegicus Kd = 25000.0 nM PMID[478547]
NPT413 Protein Complex Neuronal acetylcholine receptor Rattus norvegicus Kd = 330000.0 nM PMID[478547]
NPT413 Protein Complex Neuronal acetylcholine receptor Rattus norvegicus Kd = 41000000.0 nM PMID[478547]
NPT413 Protein Complex Neuronal acetylcholine receptor Rattus norvegicus Enhancement = 7.0 % PMID[478547]
NPT413 Protein Complex Neuronal acetylcholine receptor Rattus norvegicus Inhibition = 111.0 % PMID[478547]
NPT413 Protein Complex Neuronal acetylcholine receptor Rattus norvegicus Mean enhancement of binding = 4.5 n.a. PMID[478547]
NPT35 Others n.a. pKa = 11.27 n.a. PMID[478550]
NPT35 Others n.a. pKa n.a. 11.3 n.a. PMID[478552]
NPT35 Others n.a. T1/2 = 7.7 hr PMID[478553]

☑ 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 NPC232311 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
0.7931 Intermediate Similarity NPC193536
0.7931 Intermediate Similarity NPC152949
0.7931 Intermediate Similarity NPC270175
0.7586 Intermediate Similarity NPC27675
0.7419 Intermediate Similarity NPC21157
0.7419 Intermediate Similarity NPC95589
0.7407 Intermediate Similarity NPC119368
0.7188 Intermediate Similarity NPC320889
0.6667 Remote Similarity NPC28081
0.6667 Remote Similarity NPC309330
0.6667 Remote Similarity NPC27869
0.6389 Remote Similarity NPC74599
0.6389 Remote Similarity NPC203203
0.6207 Remote Similarity NPC306277
0.6111 Remote Similarity NPC163099
0.6053 Remote Similarity NPC473035
0.6053 Remote Similarity NPC326791
0.6 Remote Similarity NPC83032
0.6 Remote Similarity NPC125872
0.5897 Remote Similarity NPC240230
0.5897 Remote Similarity NPC167301
0.5882 Remote Similarity NPC278821
0.575 Remote Similarity NPC321202
0.5714 Remote Similarity NPC309715
0.5641 Remote Similarity NPC270319
0.561 Remote Similarity NPC319114
0.561 Remote Similarity NPC15231

  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 NPC232311 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
0.7419 Intermediate Similarity NPD401 Approved
0.6667 Remote Similarity NPD1156 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8560 Clinical (unspecified phase)
0.6471 Remote Similarity NPD2276 Clinical (unspecified phase)
0.6452 Remote Similarity NPD9063 Approved
0.6452 Remote Similarity NPD9064 Approved
0.625 Remote Similarity NPD9465 Approved
0.625 Remote Similarity NPD8544 Approved
0.6129 Remote Similarity NPD8791 Clinical (unspecified phase)
0.6053 Remote Similarity NPD2707 Clinical (unspecified phase)
0.5789 Remote Similarity NPD9059 Approved
0.575 Remote Similarity NPD2273 Clinical (unspecified phase)
0.5676 Remote Similarity NPD1832 Approved
0.5676 Remote Similarity NPD1833 Approved
0.561 Remote Similarity NPD9227 Discontinued

  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