Structure

Physi-Chem Properties

Molecular Weight:  423.11
Volume:  403.067
LogP:  1.679
LogD:  2.061
LogS:  -4.49
# Rotatable Bonds:  5
TPSA:  157.5
# H-Bond Aceptor:  10
# H-Bond Donor:  5
# Rings:  4
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.307
Synthetic Accessibility Score:  2.768
Fsp3:  0.095
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.882
MDCK Permeability:  6.641053914790973e-06
Pgp-inhibitor:  0.747
Pgp-substrate:  0.645
Human Intestinal Absorption (HIA):  0.942
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.566

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  95.90489959716797%
Volume Distribution (VD):  0.485
Pgp-substrate:  6.693985939025879%

ADMET: Metabolism

CYP1A2-inhibitor:  0.919
CYP1A2-substrate:  0.977
CYP2C19-inhibitor:  0.278
CYP2C19-substrate:  0.045
CYP2C9-inhibitor:  0.712
CYP2C9-substrate:  0.054
CYP2D6-inhibitor:  0.05
CYP2D6-substrate:  0.036
CYP3A4-inhibitor:  0.741
CYP3A4-substrate:  0.646

ADMET: Excretion

Clearance (CL):  9.465
Half-life (T1/2):  0.939

ADMET: Toxicity

hERG Blockers:  0.169
Human Hepatotoxicity (H-HT):  0.807
Drug-inuced Liver Injury (DILI):  0.991
AMES Toxicity:  0.376
Rat Oral Acute Toxicity:  0.038
Maximum Recommended Daily Dose:  0.144
Skin Sensitization:  0.027
Carcinogencity:  0.051
Eye Corrosion:  0.003
Eye Irritation:  0.031
Respiratory Toxicity:  0.835

Download Data

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

  Natural Product: NPC51846

Natural Product ID:  NPC51846
Common Name*:   6-Oxopyran-3-Carboxylic Acid
IUPAC Name:   6-oxopyran-3-carboxylic acid
Synonyms:  
Standard InCHIKey:  ORGPJDKNYMVLFL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H4O4/c7-5-2-1-4(3-10-5)6(8)9/h1-3H,(H,8,9)
SMILES:  O=c1ccc(co1)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL216734
PubChem CID:   68141
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
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25333853]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]

☑ 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
NPT2 Others Unspecified Ki = 2000000.0 nM PMID[502309]

☑ 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 NPC51846 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
0.8305 Intermediate Similarity NPC98519
0.8 Intermediate Similarity NPC309408
0.8 Intermediate Similarity NPC130953
0.7966 Intermediate Similarity NPC189700
0.7931 Intermediate Similarity NPC150717
0.7903 Intermediate Similarity NPC471611
0.7895 Intermediate Similarity NPC218486
0.7742 Intermediate Similarity NPC2328
0.7727 Intermediate Similarity NPC59558
0.7627 Intermediate Similarity NPC221763
0.7544 Intermediate Similarity NPC191643
0.75 Intermediate Similarity NPC471566
0.75 Intermediate Similarity NPC471565
0.75 Intermediate Similarity NPC273600
0.7377 Intermediate Similarity NPC254095
0.7368 Intermediate Similarity NPC43053
0.7321 Intermediate Similarity NPC126184
0.7321 Intermediate Similarity NPC234084
0.7273 Intermediate Similarity NPC132286
0.7231 Intermediate Similarity NPC471556
0.7213 Intermediate Similarity NPC249850
0.7213 Intermediate Similarity NPC293437
0.7213 Intermediate Similarity NPC135863
0.7193 Intermediate Similarity NPC15789
0.7193 Intermediate Similarity NPC221467
0.7188 Intermediate Similarity NPC473737
0.7183 Intermediate Similarity NPC470705
0.7167 Intermediate Similarity NPC173157
0.7164 Intermediate Similarity NPC238223
0.7121 Intermediate Similarity NPC470033
0.7121 Intermediate Similarity NPC475555
0.7121 Intermediate Similarity NPC475675
0.7097 Intermediate Similarity NPC223679
0.7018 Intermediate Similarity NPC122212
0.7018 Intermediate Similarity NPC137419
0.7 Intermediate Similarity NPC316851
0.7 Intermediate Similarity NPC478120
0.6984 Remote Similarity NPC302564
0.6984 Remote Similarity NPC82465
0.697 Remote Similarity NPC7940
0.6964 Remote Similarity NPC87137
0.6935 Remote Similarity NPC294938
0.6935 Remote Similarity NPC129150
0.6912 Remote Similarity NPC477117
0.6897 Remote Similarity NPC275316
0.6866 Remote Similarity NPC37382
0.6857 Remote Similarity NPC178575
0.6842 Remote Similarity NPC128520
0.6833 Remote Similarity NPC116366
0.6825 Remote Similarity NPC21946
0.6806 Remote Similarity NPC478195
0.6806 Remote Similarity NPC478194
0.6806 Remote Similarity NPC478193
0.6806 Remote Similarity NPC478196
0.6806 Remote Similarity NPC315552
0.6806 Remote Similarity NPC478192
0.6806 Remote Similarity NPC478191
0.6769 Remote Similarity NPC15193
0.6721 Remote Similarity NPC135537
0.6719 Remote Similarity NPC133600
0.6716 Remote Similarity NPC476589
0.6716 Remote Similarity NPC96414
0.6714 Remote Similarity NPC202011
0.6714 Remote Similarity NPC315597
0.6714 Remote Similarity NPC315285
0.6667 Remote Similarity NPC475073
0.6667 Remote Similarity NPC287705
0.6667 Remote Similarity NPC68110
0.6622 Remote Similarity NPC315394
0.662 Remote Similarity NPC316185
0.6618 Remote Similarity NPC146811
0.6618 Remote Similarity NPC315115
0.6618 Remote Similarity NPC201356
0.661 Remote Similarity NPC236338
0.6604 Remote Similarity NPC298413
0.6575 Remote Similarity NPC161038
0.6571 Remote Similarity NPC151481
0.6545 Remote Similarity NPC41409
0.6538 Remote Similarity NPC107877
0.6508 Remote Similarity NPC86948
0.6508 Remote Similarity NPC230296
0.6491 Remote Similarity NPC158853
0.6481 Remote Similarity NPC8270
0.6462 Remote Similarity NPC97570
0.6441 Remote Similarity NPC313553
0.6438 Remote Similarity NPC315843
0.6429 Remote Similarity NPC474823
0.6429 Remote Similarity NPC63873
0.6429 Remote Similarity NPC313444
0.6418 Remote Similarity NPC210303
0.6418 Remote Similarity NPC44343
0.6418 Remote Similarity NPC179087
0.64 Remote Similarity NPC275530
0.6389 Remote Similarity NPC293114
0.6364 Remote Similarity NPC476585
0.6364 Remote Similarity NPC221250
0.6364 Remote Similarity NPC429928
0.6349 Remote Similarity NPC478117
0.6338 Remote Similarity NPC475004
0.6324 Remote Similarity NPC475618
0.6301 Remote Similarity NPC284006
0.6286 Remote Similarity NPC122627
0.6269 Remote Similarity NPC263732
0.6269 Remote Similarity NPC26810
0.625 Remote Similarity NPC472808
0.625 Remote Similarity NPC324224
0.625 Remote Similarity NPC316029
0.625 Remote Similarity NPC476037
0.6232 Remote Similarity NPC19769
0.6232 Remote Similarity NPC282760
0.6232 Remote Similarity NPC182794
0.6232 Remote Similarity NPC470123
0.6216 Remote Similarity NPC107654
0.6216 Remote Similarity NPC470686
0.6212 Remote Similarity NPC86789
0.6207 Remote Similarity NPC270706
0.6197 Remote Similarity NPC79220
0.6197 Remote Similarity NPC280374
0.619 Remote Similarity NPC474127
0.6184 Remote Similarity NPC475711
0.6164 Remote Similarity NPC133098
0.6154 Remote Similarity NPC283502
0.6133 Remote Similarity NPC260396
0.6125 Remote Similarity NPC16488
0.6119 Remote Similarity NPC26223
0.6119 Remote Similarity NPC79756
0.6111 Remote Similarity NPC473277
0.6111 Remote Similarity NPC475982
0.6111 Remote Similarity NPC63598
0.6104 Remote Similarity NPC28049
0.6102 Remote Similarity NPC128280
0.6098 Remote Similarity NPC315395
0.6098 Remote Similarity NPC316426
0.6094 Remote Similarity NPC25038
0.6087 Remote Similarity NPC470808
0.6081 Remote Similarity NPC12815
0.6081 Remote Similarity NPC329890
0.6081 Remote Similarity NPC215745
0.6081 Remote Similarity NPC238948
0.6061 Remote Similarity NPC471619
0.6061 Remote Similarity NPC474084
0.6056 Remote Similarity NPC225272
0.6053 Remote Similarity NPC203277
0.6053 Remote Similarity NPC127118
0.6053 Remote Similarity NPC209113
0.6034 Remote Similarity NPC6963
0.6034 Remote Similarity NPC304079
0.6029 Remote Similarity NPC55376
0.6027 Remote Similarity NPC476012
0.6 Remote Similarity NPC476590
0.6 Remote Similarity NPC114727
0.6 Remote Similarity NPC313677
0.6 Remote Similarity NPC147824
0.6 Remote Similarity NPC476586
0.6 Remote Similarity NPC133904
0.5974 Remote Similarity NPC316324
0.597 Remote Similarity NPC322186
0.597 Remote Similarity NPC159650
0.597 Remote Similarity NPC22897
0.5965 Remote Similarity NPC57923
0.5965 Remote Similarity NPC169098
0.5962 Remote Similarity NPC98098
0.5962 Remote Similarity NPC224651
0.5952 Remote Similarity NPC26078
0.5952 Remote Similarity NPC473658
0.5949 Remote Similarity NPC121374
0.5942 Remote Similarity NPC132243
0.5942 Remote Similarity NPC476584
0.5938 Remote Similarity NPC129710
0.5932 Remote Similarity NPC26600
0.5932 Remote Similarity NPC47946
0.593 Remote Similarity NPC32552
0.5926 Remote Similarity NPC44261
0.5926 Remote Similarity NPC211455
0.5926 Remote Similarity NPC188717
0.5926 Remote Similarity NPC315559
0.5921 Remote Similarity NPC68624
0.5915 Remote Similarity NPC276299
0.5909 Remote Similarity NPC71755
0.5904 Remote Similarity NPC211892
0.5902 Remote Similarity NPC135698
0.5897 Remote Similarity NPC473471
0.5897 Remote Similarity NPC279532
0.5897 Remote Similarity NPC264391
0.5893 Remote Similarity NPC2741
0.5893 Remote Similarity NPC281043
0.589 Remote Similarity NPC236208
0.589 Remote Similarity NPC470693
0.5882 Remote Similarity NPC51358
0.5882 Remote Similarity NPC307092
0.5882 Remote Similarity NPC305973
0.5867 Remote Similarity NPC185186
0.5867 Remote Similarity NPC329914
0.5867 Remote Similarity NPC327383
0.5862 Remote Similarity NPC282644
0.5862 Remote Similarity NPC29798
0.5862 Remote Similarity NPC40805
0.5857 Remote Similarity NPC25747
0.5857 Remote Similarity NPC308457
0.5857 Remote Similarity NPC148233

  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 NPC51846 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
0.6491 Remote Similarity NPD9090 Phase 3
0.6441 Remote Similarity NPD4220 Pre-registration
0.6184 Remote Similarity NPD4756 Discovery
0.614 Remote Similarity NPD9411 Phase 1
0.5965 Remote Similarity NPD9091 Suspended
0.5965 Remote Similarity NPD9297 Discontinued
0.5962 Remote Similarity NPD8573 Approved
0.5926 Remote Similarity NPD9115 Approved
0.5797 Remote Similarity NPD9418 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6927 Phase 3
0.5672 Remote Similarity NPD9118 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