Structure

Physi-Chem Properties

Molecular Weight:  126.07
Volume:  133.379
LogP:  0.45
LogD:  0.695
LogS:  -0.599
# Rotatable Bonds:  1
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.56
Synthetic Accessibility Score:  2.933
Fsp3:  0.571
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:  -4.406
MDCK Permeability:  2.1104180632391945e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.035
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.964
Plasma Protein Binding (PPB):  40.52811050415039%
Volume Distribution (VD):  0.554
Pgp-substrate:  68.78691101074219%

ADMET: Metabolism

CYP1A2-inhibitor:  0.15
CYP1A2-substrate:  0.214
CYP2C19-inhibitor:  0.04
CYP2C19-substrate:  0.544
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.19
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.348
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.263

ADMET: Excretion

Clearance (CL):  6.188
Half-life (T1/2):  0.863

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.041
Drug-inuced Liver Injury (DILI):  0.166
AMES Toxicity:  0.534
Rat Oral Acute Toxicity:  0.319
Maximum Recommended Daily Dose:  0.171
Skin Sensitization:  0.778
Carcinogencity:  0.589
Eye Corrosion:  0.698
Eye Irritation:  0.991
Respiratory Toxicity:  0.406

Download Data

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

  Natural Product: NPC40148

Natural Product ID:  NPC40148
Common Name*:   2-Hydroxymethyl-3-Methylcyclopent-2-Enone
IUPAC Name:   2-(hydroxymethyl)-3-methylcyclopent-2-en-1-one
Synonyms:  
Standard InCHIKey:  VBOYONXEJMSAAT-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H10O2/c1-5-2-3-7(9)6(5)4-8/h8H,2-4H2,1H3
SMILES:  CC1=C(CO)C(=O)CC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL458459
PubChem CID:   15768146
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones

*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
NPO32737 mitosporic dothideomycete sp. lrub20 Species n.a. n.a. n.a. n.a. n.a. PMID[16989533]

☑ 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
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 200.0 ug.mL-1 PMID[470285]

☑ 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 NPC40148 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
0.7656 Intermediate Similarity NPC472072
0.7313 Intermediate Similarity NPC236208
0.7288 Intermediate Similarity NPC189677
0.7231 Intermediate Similarity NPC474329
0.7231 Intermediate Similarity NPC474304
0.7164 Intermediate Similarity NPC309466
0.7143 Intermediate Similarity NPC227396
0.7123 Intermediate Similarity NPC258231
0.7119 Intermediate Similarity NPC217188
0.7 Intermediate Similarity NPC144419
0.7 Intermediate Similarity NPC275098
0.6935 Remote Similarity NPC268185
0.6935 Remote Similarity NPC192843
0.6912 Remote Similarity NPC477452
0.6901 Remote Similarity NPC7382
0.6857 Remote Similarity NPC67076
0.6857 Remote Similarity NPC319163
0.6849 Remote Similarity NPC473536
0.6849 Remote Similarity NPC86917
0.6806 Remote Similarity NPC89374
0.6806 Remote Similarity NPC474011
0.6769 Remote Similarity NPC260573
0.6769 Remote Similarity NPC269737
0.6769 Remote Similarity NPC64985
0.6765 Remote Similarity NPC269985
0.6761 Remote Similarity NPC186042
0.6724 Remote Similarity NPC267110
0.6714 Remote Similarity NPC280256
0.6712 Remote Similarity NPC182848
0.6667 Remote Similarity NPC177030
0.6667 Remote Similarity NPC45264
0.6667 Remote Similarity NPC215050
0.6667 Remote Similarity NPC190049
0.6667 Remote Similarity NPC281230
0.6622 Remote Similarity NPC272267
0.662 Remote Similarity NPC106309
0.6613 Remote Similarity NPC317899
0.661 Remote Similarity NPC288381
0.661 Remote Similarity NPC225974
0.661 Remote Similarity NPC20934
0.6582 Remote Similarity NPC179006
0.6582 Remote Similarity NPC474853
0.6579 Remote Similarity NPC45495
0.6579 Remote Similarity NPC47653
0.6571 Remote Similarity NPC143396
0.6571 Remote Similarity NPC67608
0.6562 Remote Similarity NPC320421
0.6557 Remote Similarity NPC474496
0.6533 Remote Similarity NPC476627
0.6533 Remote Similarity NPC478122
0.6533 Remote Similarity NPC192006
0.6528 Remote Similarity NPC238948
0.6528 Remote Similarity NPC215745
0.6528 Remote Similarity NPC12815
0.6522 Remote Similarity NPC106613
0.65 Remote Similarity NPC476043
0.65 Remote Similarity NPC194417
0.65 Remote Similarity NPC15129
0.6486 Remote Similarity NPC225022
0.6486 Remote Similarity NPC474197
0.6486 Remote Similarity NPC238554
0.6486 Remote Similarity NPC256640
0.6486 Remote Similarity NPC205615
0.6486 Remote Similarity NPC16279
0.6486 Remote Similarity NPC469646
0.6479 Remote Similarity NPC318766
0.6452 Remote Similarity NPC154626
0.6447 Remote Similarity NPC476624
0.6447 Remote Similarity NPC472013
0.6447 Remote Similarity NPC301769
0.6447 Remote Similarity NPC7232
0.6447 Remote Similarity NPC32758
0.641 Remote Similarity NPC469833
0.641 Remote Similarity NPC47450
0.641 Remote Similarity NPC469838
0.6406 Remote Similarity NPC71755
0.64 Remote Similarity NPC228902
0.64 Remote Similarity NPC471061
0.64 Remote Similarity NPC24827
0.6389 Remote Similarity NPC469836
0.6389 Remote Similarity NPC29328
0.6375 Remote Similarity NPC68303
0.6375 Remote Similarity NPC307126
0.6364 Remote Similarity NPC138492
0.6364 Remote Similarity NPC233352
0.6364 Remote Similarity NPC327112
0.6364 Remote Similarity NPC287817
0.6364 Remote Similarity NPC824
0.6364 Remote Similarity NPC162741
0.6364 Remote Similarity NPC91332
0.6364 Remote Similarity NPC74445
0.6351 Remote Similarity NPC260396
0.6341 Remote Similarity NPC474854
0.6338 Remote Similarity NPC475004
0.6329 Remote Similarity NPC185256
0.6324 Remote Similarity NPC470320
0.6316 Remote Similarity NPC102065
0.6316 Remote Similarity NPC85743
0.6316 Remote Similarity NPC475994
0.6301 Remote Similarity NPC323437
0.6301 Remote Similarity NPC201562
0.6301 Remote Similarity NPC29542
0.6286 Remote Similarity NPC476626
0.6282 Remote Similarity NPC221510
0.6282 Remote Similarity NPC159714
0.6282 Remote Similarity NPC171665
0.6269 Remote Similarity NPC113293
0.6269 Remote Similarity NPC477829
0.6267 Remote Similarity NPC4492
0.6267 Remote Similarity NPC51391
0.6267 Remote Similarity NPC263582
0.6265 Remote Similarity NPC170775
0.625 Remote Similarity NPC477455
0.625 Remote Similarity NPC173321
0.625 Remote Similarity NPC469809
0.625 Remote Similarity NPC203819
0.6234 Remote Similarity NPC286816
0.6234 Remote Similarity NPC201225
0.6234 Remote Similarity NPC308038
0.6234 Remote Similarity NPC199134
0.6234 Remote Similarity NPC281138
0.6232 Remote Similarity NPC245947
0.6232 Remote Similarity NPC136164
0.6232 Remote Similarity NPC255863
0.623 Remote Similarity NPC473672
0.623 Remote Similarity NPC474495
0.622 Remote Similarity NPC72513
0.6216 Remote Similarity NPC227814
0.6216 Remote Similarity NPC469835
0.6216 Remote Similarity NPC144995
0.6212 Remote Similarity NPC318306
0.6212 Remote Similarity NPC278202
0.6203 Remote Similarity NPC253364
0.6203 Remote Similarity NPC133844
0.6203 Remote Similarity NPC20262
0.6203 Remote Similarity NPC256750
0.6197 Remote Similarity NPC474823
0.6197 Remote Similarity NPC469679
0.6197 Remote Similarity NPC117804
0.619 Remote Similarity NPC106510
0.619 Remote Similarity NPC77337
0.619 Remote Similarity NPC71533
0.6184 Remote Similarity NPC7563
0.6184 Remote Similarity NPC116177
0.6184 Remote Similarity NPC320630
0.6176 Remote Similarity NPC143168
0.6176 Remote Similarity NPC477830
0.6176 Remote Similarity NPC68110
0.6176 Remote Similarity NPC53109
0.6176 Remote Similarity NPC477707
0.6173 Remote Similarity NPC470755
0.6173 Remote Similarity NPC187529
0.6173 Remote Similarity NPC15807
0.6173 Remote Similarity NPC125290
0.6173 Remote Similarity NPC261380
0.6154 Remote Similarity NPC470945
0.6154 Remote Similarity NPC193975
0.6154 Remote Similarity NPC472948
0.6154 Remote Similarity NPC470947
0.6154 Remote Similarity NPC104120
0.6154 Remote Similarity NPC157895
0.6154 Remote Similarity NPC470946
0.6154 Remote Similarity NPC148685
0.6143 Remote Similarity NPC137163
0.6143 Remote Similarity NPC322035
0.6143 Remote Similarity NPC308294
0.6143 Remote Similarity NPC142423
0.6143 Remote Similarity NPC166791
0.6143 Remote Similarity NPC100719
0.614 Remote Similarity NPC76051
0.6133 Remote Similarity NPC474885
0.6125 Remote Similarity NPC477786
0.6125 Remote Similarity NPC477784
0.6125 Remote Similarity NPC477785
0.6111 Remote Similarity NPC470436
0.6111 Remote Similarity NPC94488
0.6111 Remote Similarity NPC250928
0.6111 Remote Similarity NPC10758
0.6111 Remote Similarity NPC473277
0.6104 Remote Similarity NPC248624
0.6104 Remote Similarity NPC108816
0.6104 Remote Similarity NPC93763
0.6104 Remote Similarity NPC62336
0.6104 Remote Similarity NPC264391
0.6104 Remote Similarity NPC172066
0.6104 Remote Similarity NPC315765
0.6104 Remote Similarity NPC178852
0.6104 Remote Similarity NPC471465
0.6104 Remote Similarity NPC196653
0.6104 Remote Similarity NPC231739
0.6102 Remote Similarity NPC471752
0.6102 Remote Similarity NPC100380
0.6098 Remote Similarity NPC261721
0.6094 Remote Similarity NPC49028
0.6087 Remote Similarity NPC7029
0.6087 Remote Similarity NPC226592
0.6081 Remote Similarity NPC247586
0.6076 Remote Similarity NPC47031
0.6076 Remote Similarity NPC150502
0.6076 Remote Similarity NPC470298

  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 NPC40148 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
0.6618 Remote Similarity NPD3704 Approved
0.6364 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6349 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6176 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6173 Remote Similarity NPD1696 Phase 3
0.6173 Remote Similarity NPD5363 Approved
0.614 Remote Similarity NPD9411 Phase 1
0.6 Remote Similarity NPD7341 Phase 2
0.6 Remote Similarity NPD4800 Clinical (unspecified phase)
0.6 Remote Similarity NPD4269 Approved
0.6 Remote Similarity NPD4270 Approved
0.5974 Remote Similarity NPD4756 Discovery
0.5949 Remote Similarity NPD4252 Approved
0.5932 Remote Similarity NPD4265 Approved
0.5915 Remote Similarity NPD7331 Phase 2
0.5846 Remote Similarity NPD342 Phase 1
0.5814 Remote Similarity NPD5785 Approved
0.5732 Remote Similarity NPD7154 Phase 3
0.5732 Remote Similarity NPD5362 Discontinued
0.5714 Remote Similarity NPD5786 Approved
0.5696 Remote Similarity NPD4271 Approved
0.5696 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5696 Remote Similarity NPD4268 Approved
0.5634 Remote Similarity NPD3197 Phase 1
0.5616 Remote Similarity NPD4247 Clinical (unspecified phase)
0.561 Remote Similarity NPD5209 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