Structure

Physi-Chem Properties

Molecular Weight:  200.0
Volume:  169.421
LogP:  0.805
LogD:  0.379
LogS:  -1.548
# Rotatable Bonds:  2
TPSA:  125.04
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.6
Synthetic Accessibility Score:  2.584
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.805
MDCK Permeability:  3.292379915365018e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.766
20% Bioavailability (F20%):  0.98
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.042
Plasma Protein Binding (PPB):  70.6051025390625%
Volume Distribution (VD):  0.474
Pgp-substrate:  31.843530654907227%

ADMET: Metabolism

CYP1A2-inhibitor:  0.027
CYP1A2-substrate:  0.046
CYP2C19-inhibitor:  0.034
CYP2C19-substrate:  0.032
CYP2C9-inhibitor:  0.029
CYP2C9-substrate:  0.069
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.08
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.011

ADMET: Excretion

Clearance (CL):  1.521
Half-life (T1/2):  0.961

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.185
Drug-inuced Liver Injury (DILI):  0.917
AMES Toxicity:  0.024
Rat Oral Acute Toxicity:  0.072
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.304
Carcinogencity:  0.027
Eye Corrosion:  0.048
Eye Irritation:  0.668
Respiratory Toxicity:  0.62

Download Data

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

  Natural Product: NPC135537

Natural Product ID:  NPC135537
Common Name*:   3-Hydroxy-4-Oxopyran-2,6-Dicarboxylic Acid
IUPAC Name:   3-hydroxy-4-oxopyran-2,6-dicarboxylic acid
Synonyms:  
Standard InCHIKey:  ZEGRKMXCOCRTCS-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H4O7/c8-2-1-3(6(10)11)14-5(4(2)9)7(12)13/h1,9H,(H,10,11)(H,12,13)/p-2
SMILES:  c1c(=O)c(c(C(=O)O)oc1C(=O)[O-])[O-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL109516
PubChem CID:   10347
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones 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
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[15019787]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[22029392]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[23517479]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota Latex Exudate n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14264 Papaver fugax Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3702 Phoebe chemensii Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3702 Phoebe chemensii Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14264 Papaver fugax Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14264 Papaver fugax Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10176 Chrozophora prostrata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7312 Aplidium multiplicatum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2466 Aloe microstigma Species Asphodelaceae 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
NPT1758 Individual Protein Hepatitis C virus NS5B RNA-dependent RNA polymerase Hepatitis C virus IC50 > 100000.0 nM PMID[506636]
NPT1758 Individual Protein Hepatitis C virus NS5B RNA-dependent RNA polymerase Hepatitis C virus IC50 = 18000.0 nM PMID[506636]
NPT191 Organism Hepatitis C virus Hepatitis C virus EC50 = 50000.0 nM PMID[506636]

☑ 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 NPC135537 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
0.8333 Intermediate Similarity NPC116366
0.7037 Intermediate Similarity NPC158853
0.6935 Remote Similarity NPC302564
0.6818 Remote Similarity NPC475675
0.6818 Remote Similarity NPC475555
0.6721 Remote Similarity NPC51846
0.6667 Remote Similarity NPC273600
0.6667 Remote Similarity NPC313553
0.6615 Remote Similarity NPC475073
0.6613 Remote Similarity NPC319423
0.6567 Remote Similarity NPC201356
0.6545 Remote Similarity NPC106547
0.6508 Remote Similarity NPC187770
0.6452 Remote Similarity NPC230296
0.6429 Remote Similarity NPC110396
0.6418 Remote Similarity NPC96414
0.6415 Remote Similarity NPC2741
0.6393 Remote Similarity NPC218486
0.6269 Remote Similarity NPC471611
0.625 Remote Similarity NPC75134
0.625 Remote Similarity NPC189700
0.6232 Remote Similarity NPC122627
0.623 Remote Similarity NPC327103
0.6216 Remote Similarity NPC470705
0.6197 Remote Similarity NPC202011
0.619 Remote Similarity NPC150717
0.6176 Remote Similarity NPC19769
0.6111 Remote Similarity NPC8270
0.6102 Remote Similarity NPC477778
0.6102 Remote Similarity NPC137419
0.6102 Remote Similarity NPC122212
0.6102 Remote Similarity NPC234084
0.6066 Remote Similarity NPC191643
0.6061 Remote Similarity NPC98519
0.6056 Remote Similarity NPC475982
0.6034 Remote Similarity NPC87137
0.6 Remote Similarity NPC221250
0.6 Remote Similarity NPC132286
0.6 Remote Similarity NPC275316
0.597 Remote Similarity NPC263732
0.5968 Remote Similarity NPC477780
0.5968 Remote Similarity NPC477781
0.5942 Remote Similarity NPC101670
0.5942 Remote Similarity NPC471556
0.5942 Remote Similarity NPC471566
0.5942 Remote Similarity NPC471565
0.5938 Remote Similarity NPC221763
0.5932 Remote Similarity NPC128520
0.5915 Remote Similarity NPC238223
0.5909 Remote Similarity NPC86789
0.5902 Remote Similarity NPC22329
0.5882 Remote Similarity NPC98098
0.5882 Remote Similarity NPC224651
0.5882 Remote Similarity NPC2328
0.5857 Remote Similarity NPC276299
0.5857 Remote Similarity NPC470033
0.5846 Remote Similarity NPC283502
0.5844 Remote Similarity NPC318481
0.5833 Remote Similarity NPC126184
0.5821 Remote Similarity NPC130953
0.5821 Remote Similarity NPC26223
0.5806 Remote Similarity NPC137396
0.5797 Remote Similarity NPC475618
0.5797 Remote Similarity NPC470808
0.5781 Remote Similarity NPC173157
0.5758 Remote Similarity NPC474084
0.5753 Remote Similarity NPC59558
0.5738 Remote Similarity NPC221467
0.5738 Remote Similarity NPC107703
0.5738 Remote Similarity NPC220191
0.5714 Remote Similarity NPC470123
0.5714 Remote Similarity NPC476589
0.5694 Remote Similarity NPC63873
0.5692 Remote Similarity NPC86948
0.5676 Remote Similarity NPC178575
0.5672 Remote Similarity NPC97570
0.5663 Remote Similarity NPC472009
0.5658 Remote Similarity NPC478196
0.5658 Remote Similarity NPC478191
0.5658 Remote Similarity NPC478195
0.5658 Remote Similarity NPC478193
0.5658 Remote Similarity NPC478192
0.5658 Remote Similarity NPC478194
0.5652 Remote Similarity NPC474774
0.5645 Remote Similarity NPC43053
0.5641 Remote Similarity NPC28049
0.5641 Remote Similarity NPC248775
0.5636 Remote Similarity NPC200147
0.5636 Remote Similarity NPC298413
0.5616 Remote Similarity NPC130618
0.5614 Remote Similarity NPC41409
0.5606 Remote Similarity NPC293437
0.5606 Remote Similarity NPC135863
0.5606 Remote Similarity NPC249850

  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 NPC135537 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
0.7037 Intermediate Similarity NPD9090 Phase 3
0.6613 Remote Similarity NPD9118 Approved
0.6508 Remote Similarity NPD69 Approved
0.6508 Remote Similarity NPD9119 Approved
0.6481 Remote Similarity NPD9297 Discontinued
0.6481 Remote Similarity NPD9091 Suspended
0.5921 Remote Similarity NPD4756 Discovery
0.5882 Remote Similarity NPD8573 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