Structure

Physi-Chem Properties

Molecular Weight:  143.09
Volume:  147.013
LogP:  -2.711
LogD:  -2.201
LogS:  -0.123
# Rotatable Bonds:  1
TPSA:  40.13
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.441
Synthetic Accessibility Score:  4.52
Fsp3:  0.857
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:  -5.596
MDCK Permeability:  0.00015817920211702585
Pgp-inhibitor:  0.0
Pgp-substrate:  0.143
Human Intestinal Absorption (HIA):  0.965
20% Bioavailability (F20%):  0.995
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.287
Plasma Protein Binding (PPB):  11.37285327911377%
Volume Distribution (VD):  0.75
Pgp-substrate:  92.36016845703125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.578
CYP2C19-inhibitor:  0.014
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.451
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.41
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.019

ADMET: Excretion

Clearance (CL):  2.491
Half-life (T1/2):  0.916

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.458
Drug-inuced Liver Injury (DILI):  0.008
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.033
Maximum Recommended Daily Dose:  0.699
Skin Sensitization:  0.086
Carcinogencity:  0.017
Eye Corrosion:  0.129
Eye Irritation:  0.387
Respiratory Toxicity:  0.307

Download Data

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

  Natural Product: NPC8488

Natural Product ID:  NPC8488
Common Name*:   1,1-Dimethylpyrrolidin-1-Ium-2-Carboxylate
IUPAC Name:   1,1-dimethylpyrrolidin-1-ium-2-carboxylate
Synonyms:  
Standard InCHIKey:  CMUNUTVVOOHQPW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H13NO2/c1-8(2)5-3-4-6(8)7(9)10/h6H,3-5H2,1-2H3
SMILES:  [O-]C(=O)C1CCC[N+]1(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1986864
PubChem CID:   554
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0004322] Proline and derivatives

*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
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. fruit n.a. PMID[10606547]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota Fruits n.a. n.a. PMID[22703163]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota Fruits n.a. n.a. PMID[24328283]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[24704554]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[32935986]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25443 Citrus reticulata Species Rutaceae 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
NPT368 Cell Line SN12C Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT370 Cell Line NCI-H23 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT369 Cell Line ACHN Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT371 Cell Line UO-31 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT372 Cell Line HOP-92 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT116 Cell Line HL-60 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT374 Cell Line SF-539 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT375 Cell Line Malme-3M Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT376 Cell Line A498 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT111 Cell Line K562 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT377 Cell Line OVCAR-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT112 Cell Line MOLT-4 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT379 Cell Line HOP-62 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT380 Cell Line U-251 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT381 Cell Line OVCAR-8 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT572 Cell Line DMS-273 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT383 Cell Line SNB-19 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT385 Cell Line SR Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT384 Cell Line TK-10 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT573 Cell Line M19-MEL Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT323 Cell Line SW-620 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT386 Cell Line KM12 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT455 Cell Line NCI-H522 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT574 Cell Line XF498 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT387 Cell Line M14 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT388 Cell Line NCI-H322M Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT389 Cell Line RPMI-8226 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT390 Cell Line LOX IMVI Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT456 Cell Line OVCAR-4 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT575 Cell Line KM-20L2 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT147 Cell Line SK-MEL-2 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT81 Cell Line A549 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT391 Cell Line HCC 2998 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT392 Cell Line SNB-75 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT148 Cell Line HCT-15 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT393 Cell Line HCT-116 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT395 Cell Line SF-268 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT394 Cell Line EKVX Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT146 Cell Line SK-OV-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT731 Cell Line LXFL 529 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT576 Cell Line DMS-114 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT397 Cell Line NCI-H460 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT398 Cell Line UACC-62 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT399 Cell Line SF-295 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT458 Cell Line IGROV-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT401 Cell Line 786-0 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT403 Cell Line UACC-257 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT578 Cell Line SNB-78 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT579 Cell Line DLD-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT404 Cell Line CCRF-CEM Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT405 Cell Line NCI-H226 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT139 Cell Line HT-29 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT170 Cell Line SK-MEL-28 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT406 Cell Line RXF 393 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT407 Cell Line COLO 205 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]
NPT732 Cell Line HOP-18 Homo sapiens GI50 n.a. 100000.0 nM PMID[483422]

☑ 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 NPC8488 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 NPC333075
1.0 High Similarity NPC274499
0.8136 Intermediate Similarity NPC160661
0.8036 Intermediate Similarity NPC302003
0.8036 Intermediate Similarity NPC245346
0.8036 Intermediate Similarity NPC11433
0.7705 Intermediate Similarity NPC287693
0.7619 Intermediate Similarity NPC322274
0.7059 Intermediate Similarity NPC327272
0.7031 Intermediate Similarity NPC78312
0.7031 Intermediate Similarity NPC221764
0.7031 Intermediate Similarity NPC135539
0.7031 Intermediate Similarity NPC196359
0.6912 Remote Similarity NPC320221
0.6818 Remote Similarity NPC15864
0.6462 Remote Similarity NPC472609
0.6452 Remote Similarity NPC268927
0.6452 Remote Similarity NPC276928
0.6452 Remote Similarity NPC64250
0.6429 Remote Similarity NPC93081
0.6429 Remote Similarity NPC140872
0.6393 Remote Similarity NPC278209
0.6308 Remote Similarity NPC57420
0.625 Remote Similarity NPC118429
0.62 Remote Similarity NPC229838
0.6182 Remote Similarity NPC327698
0.6182 Remote Similarity NPC118459
0.6164 Remote Similarity NPC59867
0.6119 Remote Similarity NPC128005
0.6119 Remote Similarity NPC84182
0.6087 Remote Similarity NPC133183
0.6061 Remote Similarity NPC226453
0.6061 Remote Similarity NPC103130
0.6042 Remote Similarity NPC59650
0.5972 Remote Similarity NPC209156
0.5972 Remote Similarity NPC256312
0.5972 Remote Similarity NPC266888
0.5972 Remote Similarity NPC161774
0.5938 Remote Similarity NPC319991
0.5915 Remote Similarity NPC196007
0.5915 Remote Similarity NPC76297
0.5915 Remote Similarity NPC214532
0.5909 Remote Similarity NPC243964
0.5902 Remote Similarity NPC183845
0.5902 Remote Similarity NPC279661
0.5882 Remote Similarity NPC327985
0.5875 Remote Similarity NPC69374
0.5875 Remote Similarity NPC90476
0.5854 Remote Similarity NPC322966
0.5844 Remote Similarity NPC475542
0.5833 Remote Similarity NPC322946
0.5818 Remote Similarity NPC276294
0.5806 Remote Similarity NPC275727
0.5763 Remote Similarity NPC226027
0.5763 Remote Similarity NPC245027
0.5763 Remote Similarity NPC316231
0.5763 Remote Similarity NPC112890
0.5763 Remote Similarity NPC43204
0.5763 Remote Similarity NPC174246
0.5763 Remote Similarity NPC62045
0.5763 Remote Similarity NPC84636
0.5763 Remote Similarity NPC162620
0.5763 Remote Similarity NPC324825
0.5738 Remote Similarity NPC189178
0.5738 Remote Similarity NPC471607
0.5738 Remote Similarity NPC263065
0.5714 Remote Similarity NPC107224
0.5714 Remote Similarity NPC198301
0.5714 Remote Similarity NPC476019
0.569 Remote Similarity NPC101249
0.566 Remote Similarity NPC234196
0.5616 Remote Similarity NPC29326
0.5606 Remote Similarity NPC177191

  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 NPC8488 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
0.8036 Intermediate Similarity NPD8865 Approved
0.75 Intermediate Similarity NPD9649 Approved
0.7231 Intermediate Similarity NPD2220 Clinical (unspecified phase)
0.7031 Intermediate Similarity NPD8868 Approved
0.6429 Remote Similarity NPD8809 Approved
0.6429 Remote Similarity NPD8808 Approved
0.6364 Remote Similarity NPD2271 Phase 3
0.625 Remote Similarity NPD9014 Approved
0.623 Remote Similarity NPD4281 Clinical (unspecified phase)
0.6061 Remote Similarity NPD9045 Approved
0.6061 Remote Similarity NPD9047 Approved
0.6061 Remote Similarity NPD9048 Approved
0.6061 Remote Similarity NPD9046 Phase 3
0.6042 Remote Similarity NPD8799 Approved
0.6042 Remote Similarity NPD8795 Approved
0.6042 Remote Similarity NPD8796 Approved
0.6034 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6029 Remote Similarity NPD9231 Phase 3
0.6029 Remote Similarity NPD9233 Phase 3
0.6029 Remote Similarity NPD9232 Phase 2
0.6 Remote Similarity NPD617 Approved
0.5974 Remote Similarity NPD1125 Discovery
0.5965 Remote Similarity NPD8973 Approved
0.5965 Remote Similarity NPD8972 Approved
0.5844 Remote Similarity NPD7763 Phase 2
0.5844 Remote Similarity NPD7762 Phase 2
0.5833 Remote Similarity NPD9441 Phase 2
0.5823 Remote Similarity NPD9577 Approved
0.58 Remote Similarity NPD8800 Approved
0.5775 Remote Similarity NPD2696 Approved
0.5775 Remote Similarity NPD2697 Approved
0.5775 Remote Similarity NPD2694 Approved
0.5775 Remote Similarity NPD2695 Approved
0.5763 Remote Similarity NPD9044 Approved
0.5763 Remote Similarity NPD9018 Approved
0.5763 Remote Similarity NPD9017 Approved
0.5738 Remote Similarity NPD9204 Approved
0.5738 Remote Similarity NPD9205 Approved
0.5714 Remote Similarity NPD2682 Approved
0.5714 Remote Similarity NPD4261 Phase 1
0.569 Remote Similarity NPD8866 Approved
0.569 Remote Similarity NPD8867 Approved
0.5679 Remote Similarity NPD7760 Phase 2
0.5679 Remote Similarity NPD7759 Phase 2
0.5625 Remote Similarity NPD9425 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