Structure

Physi-Chem Properties

Molecular Weight:  210.05
Volume:  197.809
LogP:  1.63
LogD:  1.794
LogS:  -1.977
# Rotatable Bonds:  2
TPSA:  72.81
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.816
Synthetic Accessibility Score:  3.085
Fsp3:  0.3
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:  -4.66
MDCK Permeability:  3.2447223929921165e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.026
20% Bioavailability (F20%):  0.024
30% Bioavailability (F30%):  0.821

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.024
Plasma Protein Binding (PPB):  79.78592681884766%
Volume Distribution (VD):  0.938
Pgp-substrate:  15.692874908447266%

ADMET: Metabolism

CYP1A2-inhibitor:  0.905
CYP1A2-substrate:  0.96
CYP2C19-inhibitor:  0.032
CYP2C19-substrate:  0.089
CYP2C9-inhibitor:  0.214
CYP2C9-substrate:  0.471
CYP2D6-inhibitor:  0.356
CYP2D6-substrate:  0.38
CYP3A4-inhibitor:  0.101
CYP3A4-substrate:  0.136

ADMET: Excretion

Clearance (CL):  12.153
Half-life (T1/2):  0.768

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.893
Drug-inuced Liver Injury (DILI):  0.98
AMES Toxicity:  0.072
Rat Oral Acute Toxicity:  0.678
Maximum Recommended Daily Dose:  0.092
Skin Sensitization:  0.694
Carcinogencity:  0.761
Eye Corrosion:  0.005
Eye Irritation:  0.07
Respiratory Toxicity:  0.617

Download Data

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

  Natural Product: NPC476586

Natural Product ID:  NPC476586
Common Name*:   5-(hydroxymethyl)-6-[(1S)-1-hydroxypropyl]-4-methoxy-2H-pyran-2-ol
IUPAC Name:   5-(hydroxymethyl)-6-[(1S)-1-hydroxypropyl]-4-methoxy-2H-pyran-2-ol
Synonyms:   Annularin C
Standard InCHIKey:  OEFHOBYLAXIGLN-JAVCKPHESA-N
Standard InCHI:  InChI=1S/C10H16O5/c1-3-7(12)10-6(5-11)8(14-2)4-9(13)15-10/h4,7,9,11-13H,3,5H2,1-2H3/t7-,9?/m0/s1
SMILES:  CC[C@@H](C1=C(C(=CC(O1)O)OC)CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   44566908
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans

*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
NPO33584 Annulatascus triseptatus Species Annulatascaceae Eukaryota n.a. Shaker Pond, Alfred, Maine n.a. PMID[14575427]

☑ 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
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 8 mm PMID[14575427]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 14 mm PMID[14575427]

☑ 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 NPC476586 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
0.9667 High Similarity NPC476584
0.9333 High Similarity NPC476585
0.8 Intermediate Similarity NPC178575
0.7571 Intermediate Similarity NPC238223
0.7429 Intermediate Similarity NPC132286
0.7333 Intermediate Similarity NPC470705
0.7286 Intermediate Similarity NPC470033
0.7246 Intermediate Similarity NPC90463
0.7246 Intermediate Similarity NPC471611
0.7143 Intermediate Similarity NPC273600
0.7105 Intermediate Similarity NPC229655
0.7101 Intermediate Similarity NPC475073
0.7067 Intermediate Similarity NPC472173
0.7067 Intermediate Similarity NPC472174
0.6941 Remote Similarity NPC327253
0.6933 Remote Similarity NPC132938
0.6933 Remote Similarity NPC316851
0.6901 Remote Similarity NPC7940
0.6901 Remote Similarity NPC476589
0.6892 Remote Similarity NPC59558
0.6857 Remote Similarity NPC2328
0.6806 Remote Similarity NPC201356
0.6782 Remote Similarity NPC320552
0.6753 Remote Similarity NPC478193
0.6753 Remote Similarity NPC478194
0.6753 Remote Similarity NPC315552
0.6753 Remote Similarity NPC478195
0.6753 Remote Similarity NPC478192
0.6753 Remote Similarity NPC478196
0.6753 Remote Similarity NPC206507
0.6753 Remote Similarity NPC478191
0.6753 Remote Similarity NPC147621
0.6753 Remote Similarity NPC210258
0.6714 Remote Similarity NPC15193
0.6707 Remote Similarity NPC473315
0.6707 Remote Similarity NPC142111
0.6667 Remote Similarity NPC473361
0.6667 Remote Similarity NPC96414
0.6667 Remote Similarity NPC470123
0.6667 Remote Similarity NPC302564
0.6667 Remote Similarity NPC202011
0.6667 Remote Similarity NPC329904
0.6627 Remote Similarity NPC473308
0.6627 Remote Similarity NPC136699
0.6627 Remote Similarity NPC475706
0.6627 Remote Similarity NPC220167
0.6623 Remote Similarity NPC107654
0.6623 Remote Similarity NPC315843
0.6585 Remote Similarity NPC251026
0.6575 Remote Similarity NPC475555
0.6575 Remote Similarity NPC475675
0.6571 Remote Similarity NPC258788
0.6548 Remote Similarity NPC470124
0.6548 Remote Similarity NPC73166
0.6543 Remote Similarity NPC163362
0.6543 Remote Similarity NPC127295
0.6528 Remote Similarity NPC294813
0.6528 Remote Similarity NPC13143
0.6528 Remote Similarity NPC31496
0.6479 Remote Similarity NPC55376
0.6471 Remote Similarity NPC208473
0.6463 Remote Similarity NPC246621
0.6452 Remote Similarity NPC20673
0.6444 Remote Similarity NPC170204
0.6438 Remote Similarity NPC282760
0.6438 Remote Similarity NPC471556
0.6438 Remote Similarity NPC19769
0.6438 Remote Similarity NPC471566
0.6438 Remote Similarity NPC471565
0.6429 Remote Similarity NPC475035
0.641 Remote Similarity NPC24590
0.6404 Remote Similarity NPC475098
0.6404 Remote Similarity NPC280390
0.6404 Remote Similarity NPC189651
0.64 Remote Similarity NPC63873
0.64 Remote Similarity NPC280374
0.6395 Remote Similarity NPC475186
0.6395 Remote Similarity NPC45409
0.6395 Remote Similarity NPC118077
0.6386 Remote Similarity NPC474439
0.6386 Remote Similarity NPC474028
0.6377 Remote Similarity NPC474869
0.6375 Remote Similarity NPC315394
0.6364 Remote Similarity NPC316185
0.6364 Remote Similarity NPC303451
0.6364 Remote Similarity NPC6414
0.6353 Remote Similarity NPC470658
0.6353 Remote Similarity NPC474424
0.6353 Remote Similarity NPC475034
0.6351 Remote Similarity NPC37382
0.6351 Remote Similarity NPC146811
0.6344 Remote Similarity NPC244878
0.6338 Remote Similarity NPC155457
0.6329 Remote Similarity NPC161038
0.6322 Remote Similarity NPC470137
0.631 Remote Similarity NPC315559
0.631 Remote Similarity NPC475714
0.6296 Remote Similarity NPC4436
0.625 Remote Similarity NPC326661
0.625 Remote Similarity NPC301207
0.625 Remote Similarity NPC309310
0.6237 Remote Similarity NPC151093
0.6235 Remote Similarity NPC266718
0.6235 Remote Similarity NPC126518
0.6235 Remote Similarity NPC161670
0.6222 Remote Similarity NPC61201
0.622 Remote Similarity NPC179933
0.6216 Remote Similarity NPC478098
0.6216 Remote Similarity NPC478099
0.6207 Remote Similarity NPC475037
0.6203 Remote Similarity NPC474545
0.6197 Remote Similarity NPC322186
0.619 Remote Similarity NPC313677
0.619 Remote Similarity NPC475046
0.619 Remote Similarity NPC8161
0.619 Remote Similarity NPC323251
0.619 Remote Similarity NPC310450
0.619 Remote Similarity NPC11383
0.619 Remote Similarity NPC474959
0.6184 Remote Similarity NPC272961
0.6176 Remote Similarity NPC218486
0.6173 Remote Similarity NPC49302
0.6173 Remote Similarity NPC275530
0.6173 Remote Similarity NPC125365
0.6173 Remote Similarity NPC474818
0.6173 Remote Similarity NPC51809
0.6173 Remote Similarity NPC475711
0.6173 Remote Similarity NPC176329
0.617 Remote Similarity NPC255677
0.617 Remote Similarity NPC306344
0.617 Remote Similarity NPC22149
0.6164 Remote Similarity NPC473737
0.6164 Remote Similarity NPC474723
0.6164 Remote Similarity NPC474729
0.6163 Remote Similarity NPC163606
0.6154 Remote Similarity NPC159547
0.6145 Remote Similarity NPC121374
0.6136 Remote Similarity NPC475739
0.6133 Remote Similarity NPC478101
0.6133 Remote Similarity NPC276299
0.6118 Remote Similarity NPC286770
0.6118 Remote Similarity NPC284472
0.6118 Remote Similarity NPC229799
0.6111 Remote Similarity NPC130953
0.6111 Remote Similarity NPC98519
0.6105 Remote Similarity NPC219038
0.6105 Remote Similarity NPC4637
0.6105 Remote Similarity NPC98859
0.6105 Remote Similarity NPC298255
0.6105 Remote Similarity NPC28304
0.6104 Remote Similarity NPC475982
0.6098 Remote Similarity NPC248775
0.6098 Remote Similarity NPC279214
0.6098 Remote Similarity NPC221095
0.6098 Remote Similarity NPC28049
0.6098 Remote Similarity NPC473471
0.6092 Remote Similarity NPC472379
0.6087 Remote Similarity NPC469543
0.6081 Remote Similarity NPC475221
0.6081 Remote Similarity NPC470808
0.6081 Remote Similarity NPC475618
0.6071 Remote Similarity NPC474894
0.6071 Remote Similarity NPC469469
0.6067 Remote Similarity NPC104129
0.6067 Remote Similarity NPC285588
0.6067 Remote Similarity NPC299527
0.6067 Remote Similarity NPC249408
0.6056 Remote Similarity NPC187770
0.6053 Remote Similarity NPC478100
0.6053 Remote Similarity NPC478097
0.6053 Remote Similarity NPC25298
0.6049 Remote Similarity NPC127118
0.6049 Remote Similarity NPC209113
0.6049 Remote Similarity NPC203277
0.6049 Remote Similarity NPC256720
0.6049 Remote Similarity NPC236228
0.6044 Remote Similarity NPC472196
0.6044 Remote Similarity NPC472195
0.6044 Remote Similarity NPC282644
0.6044 Remote Similarity NPC238090
0.6044 Remote Similarity NPC29798
0.6042 Remote Similarity NPC471599
0.6042 Remote Similarity NPC195510
0.6042 Remote Similarity NPC13171
0.6026 Remote Similarity NPC315285
0.6026 Remote Similarity NPC474078
0.6026 Remote Similarity NPC129630
0.6026 Remote Similarity NPC315597
0.6026 Remote Similarity NPC476037
0.6024 Remote Similarity NPC1180
0.6024 Remote Similarity NPC271632
0.6024 Remote Similarity NPC470149
0.6024 Remote Similarity NPC180725
0.6024 Remote Similarity NPC321728
0.6024 Remote Similarity NPC471537
0.6024 Remote Similarity NPC470148
0.6023 Remote Similarity NPC300779
0.6023 Remote Similarity NPC125142
0.6022 Remote Similarity NPC473333
0.6 Remote Similarity NPC474280

  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 NPC476586 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
0.7015 Intermediate Similarity NPD585 Clinical (unspecified phase)
0.6235 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6056 Remote Similarity NPD9119 Approved
0.6056 Remote Similarity NPD69 Approved
0.5915 Remote Similarity NPD9118 Approved
0.5692 Remote Similarity NPD4265 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