Structure

Physi-Chem Properties

Molecular Weight:  206.04
Volume:  183.251
LogP:  -0.409
LogD:  -0.386
LogS:  0.115
# Rotatable Bonds:  6
TPSA:  121.13
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.485
Synthetic Accessibility Score:  2.517
Fsp3:  0.571
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:  -6.052
MDCK Permeability:  0.003899170085787773
Pgp-inhibitor:  0.0
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.736
20% Bioavailability (F20%):  0.241
30% Bioavailability (F30%):  0.121

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.24
Plasma Protein Binding (PPB):  16.665363311767578%
Volume Distribution (VD):  0.301
Pgp-substrate:  72.17141723632812%

ADMET: Metabolism

CYP1A2-inhibitor:  0.004
CYP1A2-substrate:  0.06
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.829
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.134
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.005

ADMET: Excretion

Clearance (CL):  2.499
Half-life (T1/2):  0.836

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.247
Drug-inuced Liver Injury (DILI):  0.852
AMES Toxicity:  0.041
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.014
Skin Sensitization:  0.184
Carcinogencity:  0.017
Eye Corrosion:  0.911
Eye Irritation:  0.957
Respiratory Toxicity:  0.015

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

  Natural Product: NPC65985

Natural Product ID:  NPC65985
Common Name*:   3-Hydroxy-3-Methoxycarbonylpentanedioic Acid
IUPAC Name:   3-hydroxy-3-methoxycarbonylpentanedioic acid
Synonyms:  
Standard InCHIKey:  HCVBQXINVUFVCE-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H10O7/c1-14-6(12)7(13,2-4(8)9)3-5(10)11/h13H,2-3H2,1H3,(H,8,9)(H,10,11)
SMILES:  COC(=O)C(CC(=O)O)(CC(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL235362
PubChem CID:   12566215
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001986] Tricarboxylic 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
NPO19787 Citrus sinensis Species Rutaceae Eukaryota n.a. fruit n.a. PMID[10606547]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[10606602]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[11575955]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota stems Yunnan Province, China 2004 PMID[17253844]
NPO5270 Citrus natsudaidai Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[17689080]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota Stems purchased from Kyoungdong Oriental Herbal Market, Seoul, Korea 2006-APR PMID[18052323]
NPO21771 Citrus trifoliata Species Rutaceae Eukaryota n.a. fruit n.a. PMID[23872723]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota Stems n.a. n.a. PMID[27310249]
NPO21771 Citrus trifoliata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[32996318]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota Fruit Juice n.a. n.a. Database[FooDB]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota Root Bark n.a. n.a. Database[FooDB]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21771 Citrus trifoliata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5270 Citrus natsudaidai Species Rutaceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5270 Citrus natsudaidai Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21771 Citrus trifoliata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21771 Citrus trifoliata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19787 Citrus sinensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5270 Citrus natsudaidai Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7317 Citrus aurantium 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
NPT32 Organism Mus musculus Mus musculus Activity = -7.4 % PMID[532236]

☑ 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 NPC65985 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
0.9608 High Similarity NPC68743
0.9608 High Similarity NPC60830
0.9423 High Similarity NPC198377
0.9184 High Similarity NPC293378
0.9074 High Similarity NPC179624
0.8679 High Similarity NPC6883
0.8545 High Similarity NPC61567
0.8491 Intermediate Similarity NPC323401
0.8491 Intermediate Similarity NPC19676
0.7959 Intermediate Similarity NPC310220
0.7308 Intermediate Similarity NPC242655
0.7308 Intermediate Similarity NPC38891
0.72 Intermediate Similarity NPC240109
0.7188 Intermediate Similarity NPC241949
0.717 Intermediate Similarity NPC133771
0.7091 Intermediate Similarity NPC46254
0.7018 Intermediate Similarity NPC277878
0.7 Intermediate Similarity NPC293692
0.7 Intermediate Similarity NPC220922
0.6897 Remote Similarity NPC196612
0.68 Remote Similarity NPC128713
0.6731 Remote Similarity NPC121018
0.6731 Remote Similarity NPC100742
0.6731 Remote Similarity NPC192402
0.6731 Remote Similarity NPC97444
0.6731 Remote Similarity NPC19044
0.6731 Remote Similarity NPC35661
0.6731 Remote Similarity NPC24751
0.6724 Remote Similarity NPC317680
0.6667 Remote Similarity NPC270088
0.6607 Remote Similarity NPC172086
0.6607 Remote Similarity NPC247546
0.6604 Remote Similarity NPC228782
0.6604 Remote Similarity NPC313565
0.6604 Remote Similarity NPC259982
0.66 Remote Similarity NPC206924
0.6481 Remote Similarity NPC319680
0.6471 Remote Similarity NPC325454
0.6462 Remote Similarity NPC317651
0.6462 Remote Similarity NPC258690
0.6324 Remote Similarity NPC469925
0.6275 Remote Similarity NPC317945
0.625 Remote Similarity NPC323945
0.6226 Remote Similarity NPC320331
0.6154 Remote Similarity NPC38930
0.6154 Remote Similarity NPC320296
0.6122 Remote Similarity NPC125575
0.6087 Remote Similarity NPC57788
0.6087 Remote Similarity NPC32148
0.6087 Remote Similarity NPC53879
0.6078 Remote Similarity NPC1037
0.6061 Remote Similarity NPC469923
0.6038 Remote Similarity NPC222792
0.6038 Remote Similarity NPC316217
0.6027 Remote Similarity NPC125164
0.6 Remote Similarity NPC127142
0.6 Remote Similarity NPC7814
0.5932 Remote Similarity NPC328954
0.5918 Remote Similarity NPC212144
0.5789 Remote Similarity NPC474003
0.5781 Remote Similarity NPC3547
0.5769 Remote Similarity NPC5505
0.5758 Remote Similarity NPC475821
0.5758 Remote Similarity NPC17935
0.5753 Remote Similarity NPC96322
0.5686 Remote Similarity NPC307027
0.5672 Remote Similarity NPC469921
0.566 Remote Similarity NPC109026
0.5647 Remote Similarity NPC65359
0.5634 Remote Similarity NPC286842
0.5606 Remote Similarity NPC320032
0.56 Remote Similarity NPC280532

  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 NPC65985 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
0.9184 High Similarity NPD71 Approved
0.9184 High Similarity NPD9126 Approved
0.9184 High Similarity NPD9129 Approved
0.898 High Similarity NPD109 Approved
0.898 High Similarity NPD9122 Approved
0.898 High Similarity NPD108 Approved
0.898 High Similarity NPD9127 Approved
0.898 High Similarity NPD70 Approved
0.898 High Similarity NPD9123 Approved
0.898 High Similarity NPD9124 Approved
0.898 High Similarity NPD9125 Approved
0.898 High Similarity NPD9130 Phase 3
0.898 High Similarity NPD9128 Approved
0.898 High Similarity NPD9121 Approved
0.7018 Intermediate Similarity NPD9010 Approved
0.7018 Intermediate Similarity NPD9008 Approved
0.7018 Intermediate Similarity NPD9009 Approved
0.7018 Intermediate Similarity NPD64 Approved
0.7018 Intermediate Similarity NPD65 Approved
0.7018 Intermediate Similarity NPD66 Approved
0.7018 Intermediate Similarity NPD9011 Approved
0.7018 Intermediate Similarity NPD8960 Approved
0.7018 Intermediate Similarity NPD72 Approved
0.7018 Intermediate Similarity NPD9007 Approved
0.7 Intermediate Similarity NPD8959 Approved
0.6731 Remote Similarity NPD8605 Approved
0.6731 Remote Similarity NPD8602 Approved
0.6731 Remote Similarity NPD8600 Approved
0.6731 Remote Similarity NPD8599 Approved
0.6731 Remote Similarity NPD8598 Approved
0.6731 Remote Similarity NPD8601 Approved
0.6731 Remote Similarity NPD8604 Approved
0.6731 Remote Similarity NPD8603 Approved
0.6607 Remote Similarity NPD9004 Approved
0.6607 Remote Similarity NPD9005 Phase 3
0.6607 Remote Similarity NPD9003 Clinical (unspecified phase)
0.6557 Remote Similarity NPD73 Approved
0.6462 Remote Similarity NPD8961 Approved
0.6271 Remote Similarity NPD9001 Clinical (unspecified phase)
0.6271 Remote Similarity NPD9002 Approved
0.6087 Remote Similarity NPD898 Approved
0.6087 Remote Similarity NPD897 Approved
0.6087 Remote Similarity NPD896 Approved
0.6 Remote Similarity NPD8857 Approved
0.5818 Remote Similarity NPD9116 Phase 1
0.5733 Remote Similarity NPD11 Approved
0.5733 Remote Similarity NPD376 Approved
0.5672 Remote Similarity NPD9120 Clinical (unspecified phase)
0.5667 Remote Similarity NPD8964 Approved
0.5614 Remote Similarity NPD8975 Clinical (unspecified phase)

  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