Structure

Physi-Chem Properties

Molecular Weight:  180.08
Volume:  188.785
LogP:  1.899
LogD:  1.39
LogS:  -1.51
# Rotatable Bonds:  1
TPSA:  50.44
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.719
Synthetic Accessibility Score:  3.275
Fsp3:  0.3
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:  -4.641
MDCK Permeability:  1.8266238839714788e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.147

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.028
Plasma Protein Binding (PPB):  86.02594757080078%
Volume Distribution (VD):  1.075
Pgp-substrate:  23.388381958007812%

ADMET: Metabolism

CYP1A2-inhibitor:  0.802
CYP1A2-substrate:  0.918
CYP2C19-inhibitor:  0.151
CYP2C19-substrate:  0.419
CYP2C9-inhibitor:  0.135
CYP2C9-substrate:  0.696
CYP2D6-inhibitor:  0.077
CYP2D6-substrate:  0.575
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.2

ADMET: Excretion

Clearance (CL):  4.995
Half-life (T1/2):  0.856

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.325
Drug-inuced Liver Injury (DILI):  0.288
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.037
Maximum Recommended Daily Dose:  0.063
Skin Sensitization:  0.565
Carcinogencity:  0.712
Eye Corrosion:  0.477
Eye Irritation:  0.869
Respiratory Toxicity:  0.068

Download Data

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

  Natural Product: NPC218486

Natural Product ID:  NPC218486
Common Name*:   Nectriapyrone
IUPAC Name:   6-[(E)-but-2-en-2-yl]-4-hydroxy-3-methylpyran-2-one
Synonyms:  
Standard InCHIKey:  OBAWNXJOHPSFMJ-GQCTYLIASA-N
Standard InCHI:  InChI=1S/C10H12O3/c1-4-6(2)9-5-8(11)7(3)10(12)13-9/h4-5,11H,1-3H3/b6-4+
SMILES:  C/C=C(/c1cc(O)c(c(=O)o1)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3580980
PubChem CID:   54689128
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
NPO32981 cadophora sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[26035018]

☑ 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
NPT20 Organism Candida albicans Candida albicans MIC > 100.0 ug.mL-1 PMID[447964]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans MIC = 20.0 ug.mL-1 PMID[447964]

☑ 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 NPC218486 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
0.9216 High Similarity NPC191643
0.9 High Similarity NPC234084
0.9 High Similarity NPC126184
0.8704 High Similarity NPC173157
0.8621 High Similarity NPC2328
0.8571 High Similarity NPC189700
0.8545 High Similarity NPC150717
0.8545 High Similarity NPC221763
0.8431 Intermediate Similarity NPC128520
0.8333 Intermediate Similarity NPC471566
0.8333 Intermediate Similarity NPC471565
0.8333 Intermediate Similarity NPC471556
0.8276 Intermediate Similarity NPC130953
0.8197 Intermediate Similarity NPC315115
0.7966 Intermediate Similarity NPC98519
0.7937 Intermediate Similarity NPC313444
0.7895 Intermediate Similarity NPC51846
0.7797 Intermediate Similarity NPC133600
0.7778 Intermediate Similarity NPC221467
0.7692 Intermediate Similarity NPC315597
0.7692 Intermediate Similarity NPC316029
0.7692 Intermediate Similarity NPC59558
0.7586 Intermediate Similarity NPC86948
0.75 Intermediate Similarity NPC132286
0.7424 Intermediate Similarity NPC315285
0.7419 Intermediate Similarity NPC473737
0.7414 Intermediate Similarity NPC25038
0.7385 Intermediate Similarity NPC238223
0.7377 Intermediate Similarity NPC309408
0.7344 Intermediate Similarity NPC470033
0.7321 Intermediate Similarity NPC43053
0.7302 Intermediate Similarity NPC471611
0.7258 Intermediate Similarity NPC15193
0.7188 Intermediate Similarity NPC476589
0.7188 Intermediate Similarity NPC273600
0.717 Intermediate Similarity NPC6963
0.717 Intermediate Similarity NPC304079
0.7167 Intermediate Similarity NPC293437
0.7167 Intermediate Similarity NPC135863
0.7167 Intermediate Similarity NPC249850
0.7143 Intermediate Similarity NPC132243
0.7143 Intermediate Similarity NPC15789
0.7143 Intermediate Similarity NPC475073
0.7143 Intermediate Similarity NPC470705
0.7143 Intermediate Similarity NPC236338
0.7121 Intermediate Similarity NPC287705
0.7121 Intermediate Similarity NPC477117
0.7121 Intermediate Similarity NPC79220
0.7119 Intermediate Similarity NPC478117
0.7097 Intermediate Similarity NPC429928
0.7059 Intermediate Similarity NPC178575
0.7049 Intermediate Similarity NPC21946
0.7049 Intermediate Similarity NPC254095
0.7042 Intermediate Similarity NPC315394
0.7042 Intermediate Similarity NPC316324
0.7037 Intermediate Similarity NPC270706
0.7031 Intermediate Similarity NPC475618
0.7015 Intermediate Similarity NPC473277
0.6949 Remote Similarity NPC478120
0.6935 Remote Similarity NPC82465
0.6935 Remote Similarity NPC302564
0.6923 Remote Similarity NPC7940
0.6909 Remote Similarity NPC87137
0.6909 Remote Similarity NPC308331
0.6909 Remote Similarity NPC128280
0.6885 Remote Similarity NPC129150
0.6885 Remote Similarity NPC294938
0.6842 Remote Similarity NPC275316
0.6818 Remote Similarity NPC475675
0.6818 Remote Similarity NPC37382
0.6818 Remote Similarity NPC475555
0.6786 Remote Similarity NPC90490
0.6774 Remote Similarity NPC223679
0.6761 Remote Similarity NPC478192
0.6761 Remote Similarity NPC478196
0.6761 Remote Similarity NPC478191
0.6761 Remote Similarity NPC478195
0.6761 Remote Similarity NPC478194
0.6761 Remote Similarity NPC478193
0.6731 Remote Similarity NPC8270
0.6727 Remote Similarity NPC47946
0.6727 Remote Similarity NPC26600
0.6716 Remote Similarity NPC470442
0.6714 Remote Similarity NPC316851
0.6667 Remote Similarity NPC135698
0.6667 Remote Similarity NPC202011
0.6667 Remote Similarity NPC182794
0.6667 Remote Similarity NPC82446
0.6667 Remote Similarity NPC220766
0.6667 Remote Similarity NPC474127
0.662 Remote Similarity NPC470686
0.6618 Remote Similarity NPC474823
0.6618 Remote Similarity NPC280374
0.6615 Remote Similarity NPC68110
0.6615 Remote Similarity NPC210303
0.6615 Remote Similarity NPC179087
0.6615 Remote Similarity NPC44343
0.6613 Remote Similarity NPC283502
0.6613 Remote Similarity NPC474825
0.6607 Remote Similarity NPC197467
0.6604 Remote Similarity NPC221250
0.66 Remote Similarity NPC308418
0.6571 Remote Similarity NPC181587
0.6571 Remote Similarity NPC133098
0.6567 Remote Similarity NPC191233
0.6562 Remote Similarity NPC79756
0.6562 Remote Similarity NPC476585
0.6552 Remote Similarity NPC27264
0.6528 Remote Similarity NPC315552
0.6522 Remote Similarity NPC151481
0.6522 Remote Similarity NPC475004
0.6508 Remote Similarity NPC474084
0.65 Remote Similarity NPC327103
0.6481 Remote Similarity NPC57923
0.6441 Remote Similarity NPC148056
0.6438 Remote Similarity NPC263266
0.6418 Remote Similarity NPC470123
0.6418 Remote Similarity NPC96414
0.6418 Remote Similarity NPC131174
0.6418 Remote Similarity NPC282760
0.6418 Remote Similarity NPC133904
0.6406 Remote Similarity NPC286189
0.6406 Remote Similarity NPC97570
0.6393 Remote Similarity NPC135537
0.6379 Remote Similarity NPC15912
0.6364 Remote Similarity NPC476584
0.6346 Remote Similarity NPC63598
0.6338 Remote Similarity NPC316185
0.6333 Remote Similarity NPC151919
0.6324 Remote Similarity NPC469446
0.6324 Remote Similarity NPC201356
0.6324 Remote Similarity NPC146811
0.6286 Remote Similarity NPC470693
0.6286 Remote Similarity NPC232812
0.6269 Remote Similarity NPC173409
0.6269 Remote Similarity NPC53136
0.6267 Remote Similarity NPC315765
0.6232 Remote Similarity NPC225272
0.6226 Remote Similarity NPC200147
0.6212 Remote Similarity NPC326645
0.6212 Remote Similarity NPC55376
0.6212 Remote Similarity NPC270412
0.6212 Remote Similarity NPC329416
0.6212 Remote Similarity NPC217537
0.6212 Remote Similarity NPC151648
0.6212 Remote Similarity NPC26810
0.6212 Remote Similarity NPC263732
0.6212 Remote Similarity NPC317177
0.6212 Remote Similarity NPC14437
0.6212 Remote Similarity NPC317025
0.6212 Remote Similarity NPC68044
0.6197 Remote Similarity NPC37929
0.6197 Remote Similarity NPC64234
0.619 Remote Similarity NPC324224
0.619 Remote Similarity NPC230296
0.619 Remote Similarity NPC472808
0.6184 Remote Similarity NPC271632
0.6182 Remote Similarity NPC41409
0.6182 Remote Similarity NPC102879
0.6176 Remote Similarity NPC476586
0.6164 Remote Similarity NPC315843
0.6154 Remote Similarity NPC86789
0.6154 Remote Similarity NPC474439
0.6154 Remote Similarity NPC159650
0.6154 Remote Similarity NPC474028
0.6154 Remote Similarity NPC22897
0.6154 Remote Similarity NPC222852
0.6143 Remote Similarity NPC470032
0.6143 Remote Similarity NPC63873
0.6133 Remote Similarity NPC473825
0.6133 Remote Similarity NPC54996
0.6129 Remote Similarity NPC129710
0.6129 Remote Similarity NPC151761
0.6129 Remote Similarity NPC159535
0.6119 Remote Similarity NPC155849
0.6111 Remote Similarity NPC111474
0.6111 Remote Similarity NPC293114
0.6102 Remote Similarity NPC122212
0.6102 Remote Similarity NPC137419
0.6094 Remote Similarity NPC212730
0.6094 Remote Similarity NPC44542
0.6094 Remote Similarity NPC265551
0.6094 Remote Similarity NPC472445
0.6081 Remote Similarity NPC210258
0.6081 Remote Similarity NPC206507
0.6081 Remote Similarity NPC147621
0.6081 Remote Similarity NPC161038
0.6076 Remote Similarity NPC475714
0.6066 Remote Similarity NPC106531
0.6061 Remote Similarity NPC26223
0.6061 Remote Similarity NPC305973
0.6053 Remote Similarity NPC28049
0.6032 Remote Similarity NPC49028
0.6032 Remote Similarity NPC474913
0.6029 Remote Similarity NPC477456
0.6029 Remote Similarity NPC470808
0.6029 Remote Similarity NPC150162
0.6029 Remote Similarity NPC477457
0.6027 Remote Similarity NPC284006
0.6 Remote Similarity NPC225022

  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 NPC218486 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
0.7273 Intermediate Similarity NPD4220 Pre-registration
0.6667 Remote Similarity NPD9411 Phase 1
0.6441 Remote Similarity NPD6927 Phase 3
0.6212 Remote Similarity NPD4193 Approved
0.6212 Remote Similarity NPD4191 Approved
0.6212 Remote Similarity NPD9418 Clinical (unspecified phase)
0.6212 Remote Similarity NPD4194 Approved
0.6212 Remote Similarity NPD4192 Approved
0.6133 Remote Similarity NPD4756 Discovery
0.5797 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5625 Remote Similarity NPD539 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