Structure

Physi-Chem Properties

Molecular Weight:  186.09
Volume:  185.552
LogP:  0.87
LogD:  1.923
LogS:  -0.672
# Rotatable Bonds:  4
TPSA:  74.6
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.697
Synthetic Accessibility Score:  2.323
Fsp3:  0.778
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:  -5.642
MDCK Permeability:  3.015257061633747e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.054
Plasma Protein Binding (PPB):  51.408531188964844%
Volume Distribution (VD):  0.267
Pgp-substrate:  59.44331359863281%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.068
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.051
CYP2C9-inhibitor:  0.019
CYP2C9-substrate:  0.853
CYP2D6-inhibitor:  0.035
CYP2D6-substrate:  0.12
CYP3A4-inhibitor:  0.019
CYP3A4-substrate:  0.007

ADMET: Excretion

Clearance (CL):  0.608
Half-life (T1/2):  0.763

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.82
Drug-inuced Liver Injury (DILI):  0.038
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.077
Skin Sensitization:  0.031
Carcinogencity:  0.52
Eye Corrosion:  0.904
Eye Irritation:  0.973
Respiratory Toxicity:  0.112

Download Data

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

  Natural Product: NPC476469

Natural Product ID:  NPC476469
Common Name*:   3,3-Tetramethyleneglutaric Acid
IUPAC Name:   2-[1-(carboxymethyl)cyclopentyl]acetic acid
Synonyms:   3,3-Tetramethyleneglutaric Acid
Standard InCHIKey:  FWPVKDFOUXHOKQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H14O4/c10-7(11)5-9(6-8(12)13)3-1-2-4-9/h1-6H2,(H,10,11)(H,12,13)
SMILES:  C1CCC(C1)(CC(=O)O)CC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL80679
PubChem CID:   85558
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000346] Dicarboxylic acids 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
NPO32985 osteomeles schwerinae Species Rosaceae Eukaryota Leaves and Twigs n.a. n.a. PMID[26331986]

☑ 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
NPT711 Individual Protein Aldose reductase Bos taurus IC50 = 10000.0 nM PMID[487922]
NPT711 Individual Protein Aldose reductase Bos taurus IC50 = 1000.0 nM PMID[487922]
NPT29 Organism Rattus norvegicus Rattus norvegicus ED50 ~ 500.0 mg.kg-1 PMID[487922]
NPT68 Individual Protein Aldose reductase Rattus norvegicus IC50 = 31800.0 nM PMID[487923]
NPT68 Individual Protein Aldose reductase Rattus norvegicus IC50 = 28700.0 nM PMID[487924]

☑ 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 NPC476469 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
0.74 Intermediate Similarity NPC314679
0.7391 Intermediate Similarity NPC268826
0.7333 Intermediate Similarity NPC134782
0.7292 Intermediate Similarity NPC248763
0.7292 Intermediate Similarity NPC325452
0.7234 Intermediate Similarity NPC118968
0.7234 Intermediate Similarity NPC294085
0.7234 Intermediate Similarity NPC183424
0.7234 Intermediate Similarity NPC214610
0.72 Intermediate Similarity NPC55023
0.7115 Intermediate Similarity NPC324793
0.7115 Intermediate Similarity NPC477878
0.7021 Intermediate Similarity NPC325454
0.6957 Remote Similarity NPC155263
0.6923 Remote Similarity NPC21844
0.6875 Remote Similarity NPC3531
0.6875 Remote Similarity NPC154186
0.6875 Remote Similarity NPC201844
0.6875 Remote Similarity NPC261080
0.6875 Remote Similarity NPC113928
0.6875 Remote Similarity NPC14227
0.6875 Remote Similarity NPC301696
0.6875 Remote Similarity NPC301585
0.6875 Remote Similarity NPC279026
0.6833 Remote Similarity NPC469921
0.6809 Remote Similarity NPC252843
0.6786 Remote Similarity NPC72722
0.6735 Remote Similarity NPC240109
0.6667 Remote Similarity NPC319589
0.6667 Remote Similarity NPC18224
0.6667 Remote Similarity NPC469791
0.6667 Remote Similarity NPC328710
0.6667 Remote Similarity NPC125575
0.66 Remote Similarity NPC307783
0.66 Remote Similarity NPC209970
0.66 Remote Similarity NPC171736
0.66 Remote Similarity NPC149184
0.66 Remote Similarity NPC196924
0.66 Remote Similarity NPC216630
0.6567 Remote Similarity NPC472309
0.6562 Remote Similarity NPC477931
0.6562 Remote Similarity NPC268736
0.6522 Remote Similarity NPC132064
0.6471 Remote Similarity NPC310220
0.6471 Remote Similarity NPC67462
0.6471 Remote Similarity NPC289686
0.6452 Remote Similarity NPC469923
0.6441 Remote Similarity NPC473936
0.6415 Remote Similarity NPC282440
0.6415 Remote Similarity NPC166287
0.6383 Remote Similarity NPC156630
0.6364 Remote Similarity NPC470956
0.6346 Remote Similarity NPC255837
0.6346 Remote Similarity NPC74845
0.6346 Remote Similarity NPC19305
0.6338 Remote Similarity NPC169389
0.6308 Remote Similarity NPC241949
0.6308 Remote Similarity NPC42060
0.6304 Remote Similarity NPC175342
0.629 Remote Similarity NPC302188
0.6286 Remote Similarity NPC472311
0.625 Remote Similarity NPC305182
0.6226 Remote Similarity NPC8219
0.6212 Remote Similarity NPC60120
0.6212 Remote Similarity NPC478180
0.6212 Remote Similarity NPC130459
0.6212 Remote Similarity NPC474221
0.62 Remote Similarity NPC31551
0.62 Remote Similarity NPC219536
0.6154 Remote Similarity NPC476330
0.6143 Remote Similarity NPC477867
0.6143 Remote Similarity NPC125164
0.614 Remote Similarity NPC155512
0.6129 Remote Similarity NPC469924
0.6129 Remote Similarity NPC475821
0.6122 Remote Similarity NPC206924
0.6119 Remote Similarity NPC82315
0.6119 Remote Similarity NPC319007
0.6111 Remote Similarity NPC30195
0.6111 Remote Similarity NPC12438
0.6111 Remote Similarity NPC308301
0.6087 Remote Similarity NPC469940
0.6087 Remote Similarity NPC311102
0.6066 Remote Similarity NPC319279
0.6056 Remote Similarity NPC155441
0.6056 Remote Similarity NPC179922
0.6042 Remote Similarity NPC317203
0.6032 Remote Similarity NPC472328
0.6029 Remote Similarity NPC252032
0.6029 Remote Similarity NPC64466
0.6029 Remote Similarity NPC474962
0.6029 Remote Similarity NPC196197
0.6029 Remote Similarity NPC28526
0.6029 Remote Similarity NPC469941
0.6029 Remote Similarity NPC319671
0.6029 Remote Similarity NPC98711
0.6029 Remote Similarity NPC475062
0.6029 Remote Similarity NPC476734
0.6 Remote Similarity NPC54980
0.6 Remote Similarity NPC201622
0.6 Remote Similarity NPC328497
0.6 Remote Similarity NPC73245
0.6 Remote Similarity NPC305660
0.6 Remote Similarity NPC324004
0.6 Remote Similarity NPC249754
0.6 Remote Similarity NPC22903
0.597 Remote Similarity NPC286842
0.5962 Remote Similarity NPC103286
0.5962 Remote Similarity NPC53541
0.5962 Remote Similarity NPC163746
0.5946 Remote Similarity NPC472310
0.5942 Remote Similarity NPC477850
0.5942 Remote Similarity NPC108131
0.5942 Remote Similarity NPC18543
0.5942 Remote Similarity NPC477929
0.5938 Remote Similarity NPC174560
0.5938 Remote Similarity NPC125312
0.5938 Remote Similarity NPC469922
0.5915 Remote Similarity NPC477930
0.5915 Remote Similarity NPC215030
0.5909 Remote Similarity NPC19311
0.5909 Remote Similarity NPC230047
0.5909 Remote Similarity NPC157518
0.5893 Remote Similarity NPC200618
0.5893 Remote Similarity NPC106872
0.5893 Remote Similarity NPC180534
0.5893 Remote Similarity NPC131770
0.589 Remote Similarity NPC74685
0.5882 Remote Similarity NPC36616
0.5882 Remote Similarity NPC80234
0.5882 Remote Similarity NPC476629
0.5882 Remote Similarity NPC223249
0.5882 Remote Similarity NPC290445
0.5873 Remote Similarity NPC470363
0.5862 Remote Similarity NPC100096
0.5849 Remote Similarity NPC129972
0.5849 Remote Similarity NPC301528
0.5849 Remote Similarity NPC71317
0.5846 Remote Similarity NPC235788
0.5846 Remote Similarity NPC474552
0.5833 Remote Similarity NPC57499
0.5833 Remote Similarity NPC477934
0.5821 Remote Similarity NPC473899
0.5811 Remote Similarity NPC34046
0.5811 Remote Similarity NPC324700
0.5811 Remote Similarity NPC185465
0.5811 Remote Similarity NPC224802
0.5811 Remote Similarity NPC171426
0.5811 Remote Similarity NPC80089
0.58 Remote Similarity NPC109026
0.5789 Remote Similarity NPC304162
0.5789 Remote Similarity NPC293378
0.5781 Remote Similarity NPC478126
0.5775 Remote Similarity NPC330659
0.5775 Remote Similarity NPC475260
0.5775 Remote Similarity NPC161187
0.5775 Remote Similarity NPC51249
0.5775 Remote Similarity NPC473775
0.5775 Remote Similarity NPC473699
0.5775 Remote Similarity NPC244708
0.5775 Remote Similarity NPC475232
0.5775 Remote Similarity NPC177826
0.5775 Remote Similarity NPC474100
0.5769 Remote Similarity NPC40597
0.5769 Remote Similarity NPC161097
0.5769 Remote Similarity NPC165533
0.5769 Remote Similarity NPC12156
0.5769 Remote Similarity NPC28598
0.5769 Remote Similarity NPC149299
0.5769 Remote Similarity NPC250028
0.5769 Remote Similarity NPC256163
0.5758 Remote Similarity NPC128608
0.5758 Remote Similarity NPC314103
0.5758 Remote Similarity NPC53642
0.5758 Remote Similarity NPC470325
0.5758 Remote Similarity NPC234767
0.5753 Remote Similarity NPC477933
0.5753 Remote Similarity NPC4209
0.5753 Remote Similarity NPC246445
0.5753 Remote Similarity NPC477932
0.5745 Remote Similarity NPC280532
0.5741 Remote Similarity NPC317128
0.5735 Remote Similarity NPC57788
0.5735 Remote Similarity NPC53879
0.5735 Remote Similarity NPC469925
0.5735 Remote Similarity NPC41542
0.5733 Remote Similarity NPC320144
0.5733 Remote Similarity NPC201276
0.5733 Remote Similarity NPC80891
0.5714 Remote Similarity NPC30583
0.5694 Remote Similarity NPC167702
0.5694 Remote Similarity NPC280026
0.5692 Remote Similarity NPC306750
0.569 Remote Similarity NPC90904
0.569 Remote Similarity NPC50457
0.5686 Remote Similarity NPC128713
0.5686 Remote Similarity NPC326532
0.5686 Remote Similarity NPC38930
0.5676 Remote Similarity NPC180199
0.5676 Remote Similarity NPC317913

  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 NPC476469 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
0.74 Intermediate Similarity NPD634 Phase 3
0.7358 Intermediate Similarity NPD9638 Phase 2
0.7234 Intermediate Similarity NPD9655 Approved
0.7143 Intermediate Similarity NPD387 Clinical (unspecified phase)
0.6964 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6875 Remote Similarity NPD633 Phase 3
0.6875 Remote Similarity NPD77 Approved
0.6875 Remote Similarity NPD9450 Approved
0.6875 Remote Similarity NPD9448 Phase 2
0.6809 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6792 Remote Similarity NPD2266 Phase 2
0.6607 Remote Similarity NPD3186 Phase 1
0.66 Remote Similarity NPD2270 Approved
0.6508 Remote Similarity NPD7909 Approved
0.6415 Remote Similarity NPD9430 Approved
0.6415 Remote Similarity NPD9431 Approved
0.64 Remote Similarity NPD9635 Discontinued
0.6393 Remote Similarity NPD3198 Approved
0.6383 Remote Similarity NPD9447 Approved
0.6379 Remote Similarity NPD615 Clinical (unspecified phase)
0.6346 Remote Similarity NPD8975 Clinical (unspecified phase)
0.6324 Remote Similarity NPD6081 Approved
0.6308 Remote Similarity NPD9421 Phase 1
0.6308 Remote Similarity NPD4224 Phase 2
0.6308 Remote Similarity NPD375 Phase 2
0.629 Remote Similarity NPD9656 Approved
0.6275 Remote Similarity NPD9116 Phase 1
0.6226 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6226 Remote Similarity NPD8974 Clinical (unspecified phase)
0.6066 Remote Similarity NPD9438 Approved
0.6066 Remote Similarity NPD9439 Approved
0.6 Remote Similarity NPD3206 Approved
0.5893 Remote Similarity NPD622 Approved
0.5833 Remote Similarity NPD3702 Approved
0.5811 Remote Similarity NPD6115 Approved
0.5811 Remote Similarity NPD6697 Approved
0.5811 Remote Similarity NPD6118 Approved
0.5811 Remote Similarity NPD6114 Approved
0.5789 Remote Similarity NPD71 Approved
0.5789 Remote Similarity NPD9126 Approved
0.5789 Remote Similarity NPD9129 Approved
0.5753 Remote Similarity NPD6117 Approved
0.5694 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5692 Remote Similarity NPD9676 Phase 3
0.5686 Remote Similarity NPD9513 Phase 1
0.5676 Remote Similarity NPD6116 Phase 1
0.5672 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5658 Remote Similarity NPD9385 Clinical (unspecified phase)
0.5645 Remote Similarity NPD73 Approved
0.5614 Remote Similarity NPD9125 Approved
0.5614 Remote Similarity NPD9128 Approved
0.5614 Remote Similarity NPD9121 Approved
0.5614 Remote Similarity NPD9123 Approved
0.5614 Remote Similarity NPD9127 Approved
0.5614 Remote Similarity NPD109 Approved
0.5614 Remote Similarity NPD9124 Approved
0.5614 Remote Similarity NPD9122 Approved
0.5614 Remote Similarity NPD9130 Phase 3
0.5614 Remote Similarity NPD108 Approved
0.5614 Remote Similarity NPD70 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