Structure

Physi-Chem Properties

Molecular Weight:  270.18
Volume:  283.408
LogP:  0.601
LogD:  1.924
LogS:  -1.524
# Rotatable Bonds:  5
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.796
Synthetic Accessibility Score:  4.723
Fsp3:  0.933
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:  -4.794
MDCK Permeability:  2.676707117643673e-05
Pgp-inhibitor:  0.063
Pgp-substrate:  0.968
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.875
Plasma Protein Binding (PPB):  60.82303237915039%
Volume Distribution (VD):  0.797
Pgp-substrate:  41.93172073364258%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.541
CYP2C19-inhibitor:  0.013
CYP2C19-substrate:  0.854
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.079
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.175
CYP3A4-inhibitor:  0.027
CYP3A4-substrate:  0.371

ADMET: Excretion

Clearance (CL):  7.997
Half-life (T1/2):  0.875

ADMET: Toxicity

hERG Blockers:  0.078
Human Hepatotoxicity (H-HT):  0.247
Drug-inuced Liver Injury (DILI):  0.128
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.025
Maximum Recommended Daily Dose:  0.021
Skin Sensitization:  0.687
Carcinogencity:  0.519
Eye Corrosion:  0.825
Eye Irritation:  0.91
Respiratory Toxicity:  0.691

Download Data

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

  Natural Product: NPC473899

Natural Product ID:  NPC473899
Common Name*:   Dichomitone
IUPAC Name:   4-[(1R,2S,3S)-2-(hydroxymethyl)-3-[(4R,5S)-2-hydroxy-5-methyloxan-4-yl]-2-methylcyclopropyl]butan-2-one
Synonyms:   Dichomitone
Standard InCHIKey:  XWGMWDXATZANIP-KNTYYSJVSA-N
Standard InCHI:  InChI=1S/C15H26O4/c1-9-7-19-13(18)6-11(9)14-12(5-4-10(2)17)15(14,3)8-16/h9,11-14,16,18H,4-8H2,1-3H3/t9-,11+,12-,13?,14+,15+/m1/s1
SMILES:  CC1COC(CC1C2C(C2(C)CO)CCC(=O)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL454584
PubChem CID:   11265706
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002012] Oxanes

*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
NPO26683 Dichomitus squalens Species Polyporaceae Eukaryota n.a. n.a. n.a. PMID[15620268]
NPO26683 Dichomitus squalens Species Polyporaceae 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
NPT593 Organism Bursaphelenchus xylophilus Bursaphelenchus xylophilus LC50 > 1000.0 ug.mL-1 PMID[497255]

☑ 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 NPC473899 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
0.7368 Intermediate Similarity NPC70996
0.7333 Intermediate Similarity NPC179858
0.7042 Intermediate Similarity NPC476330
0.7037 Intermediate Similarity NPC474266
0.6986 Remote Similarity NPC474954
0.6914 Remote Similarity NPC475849
0.6824 Remote Similarity NPC470009
0.679 Remote Similarity NPC216941
0.6761 Remote Similarity NPC235788
0.6753 Remote Similarity NPC477867
0.6747 Remote Similarity NPC79308
0.6711 Remote Similarity NPC478227
0.6711 Remote Similarity NPC473267
0.6709 Remote Similarity NPC188793
0.6667 Remote Similarity NPC98711
0.6667 Remote Similarity NPC179922
0.6667 Remote Similarity NPC132064
0.6667 Remote Similarity NPC128608
0.6667 Remote Similarity NPC475062
0.6667 Remote Similarity NPC219495
0.663 Remote Similarity NPC41843
0.6627 Remote Similarity NPC472744
0.6625 Remote Similarity NPC475725
0.6622 Remote Similarity NPC472984
0.6622 Remote Similarity NPC286842
0.662 Remote Similarity NPC253204
0.6591 Remote Similarity NPC324157
0.6588 Remote Similarity NPC470657
0.6579 Remote Similarity NPC477850
0.6575 Remote Similarity NPC306805
0.6575 Remote Similarity NPC469791
0.6575 Remote Similarity NPC215987
0.6571 Remote Similarity NPC475821
0.6571 Remote Similarity NPC470363
0.6556 Remote Similarity NPC108141
0.6548 Remote Similarity NPC51135
0.6548 Remote Similarity NPC101138
0.6548 Remote Similarity NPC82492
0.6548 Remote Similarity NPC25802
0.6538 Remote Similarity NPC317212
0.6538 Remote Similarity NPC308489
0.6533 Remote Similarity NPC103647
0.6533 Remote Similarity NPC319007
0.6533 Remote Similarity NPC2568
0.6533 Remote Similarity NPC180777
0.6533 Remote Similarity NPC260319
0.6528 Remote Similarity NPC474552
0.6528 Remote Similarity NPC325773
0.6512 Remote Similarity NPC31349
0.65 Remote Similarity NPC83108
0.65 Remote Similarity NPC264602
0.65 Remote Similarity NPC169389
0.65 Remote Similarity NPC214030
0.65 Remote Similarity NPC307865
0.65 Remote Similarity NPC477918
0.6494 Remote Similarity NPC185419
0.6494 Remote Similarity NPC184550
0.6494 Remote Similarity NPC469940
0.6484 Remote Similarity NPC193785
0.6471 Remote Similarity NPC477205
0.6471 Remote Similarity NPC478111
0.6456 Remote Similarity NPC273366
0.6456 Remote Similarity NPC472311
0.6447 Remote Similarity NPC131892
0.6447 Remote Similarity NPC213178
0.6447 Remote Similarity NPC6120
0.6447 Remote Similarity NPC327728
0.6447 Remote Similarity NPC324607
0.6447 Remote Similarity NPC321732
0.6438 Remote Similarity NPC314103
0.6437 Remote Similarity NPC33398
0.6429 Remote Similarity NPC227170
0.6413 Remote Similarity NPC278506
0.641 Remote Similarity NPC291228
0.641 Remote Similarity NPC308096
0.6406 Remote Similarity NPC13105
0.6404 Remote Similarity NPC475878
0.64 Remote Similarity NPC206601
0.64 Remote Similarity NPC41542
0.6395 Remote Similarity NPC474448
0.6395 Remote Similarity NPC248216
0.6395 Remote Similarity NPC472745
0.6389 Remote Similarity NPC306750
0.6386 Remote Similarity NPC475743
0.6386 Remote Similarity NPC474870
0.6386 Remote Similarity NPC469745
0.6386 Remote Similarity NPC271572
0.6375 Remote Similarity NPC477932
0.6375 Remote Similarity NPC474020
0.6375 Remote Similarity NPC477933
0.6374 Remote Similarity NPC215570
0.6364 Remote Similarity NPC476731
0.6364 Remote Similarity NPC477929
0.6364 Remote Similarity NPC470268
0.6364 Remote Similarity NPC471879
0.6364 Remote Similarity NPC314084
0.6353 Remote Similarity NPC477434
0.6353 Remote Similarity NPC319909
0.6353 Remote Similarity NPC219535
0.6353 Remote Similarity NPC237938
0.6353 Remote Similarity NPC475689
0.6353 Remote Similarity NPC471044
0.6353 Remote Similarity NPC473336
0.6351 Remote Similarity NPC157518
0.6349 Remote Similarity NPC314679
0.6344 Remote Similarity NPC469565
0.6344 Remote Similarity NPC70733
0.6344 Remote Similarity NPC56071
0.6341 Remote Similarity NPC80891
0.6341 Remote Similarity NPC201276
0.6341 Remote Similarity NPC275243
0.6341 Remote Similarity NPC52951
0.6338 Remote Similarity NPC469924
0.6333 Remote Similarity NPC161035
0.6329 Remote Similarity NPC215030
0.6322 Remote Similarity NPC230016
0.6322 Remote Similarity NPC475773
0.6322 Remote Similarity NPC470920
0.6316 Remote Similarity NPC470956
0.6316 Remote Similarity NPC478228
0.6316 Remote Similarity NPC82315
0.631 Remote Similarity NPC164289
0.631 Remote Similarity NPC100366
0.631 Remote Similarity NPC289486
0.631 Remote Similarity NPC311642
0.631 Remote Similarity NPC242771
0.631 Remote Similarity NPC61107
0.631 Remote Similarity NPC212340
0.6296 Remote Similarity NPC474404
0.6296 Remote Similarity NPC474003
0.6296 Remote Similarity NPC475031
0.6296 Remote Similarity NPC469867
0.6292 Remote Similarity NPC77756
0.6282 Remote Similarity NPC151018
0.6282 Remote Similarity NPC320549
0.6282 Remote Similarity NPC290058
0.6282 Remote Similarity NPC58057
0.6282 Remote Similarity NPC156277
0.6282 Remote Similarity NPC89310
0.6279 Remote Similarity NPC477445
0.6279 Remote Similarity NPC473350
0.6277 Remote Similarity NPC80417
0.6277 Remote Similarity NPC20028
0.6265 Remote Similarity NPC477851
0.6265 Remote Similarity NPC472853
0.6265 Remote Similarity NPC60568
0.625 Remote Similarity NPC475412
0.625 Remote Similarity NPC236459
0.625 Remote Similarity NPC34562
0.625 Remote Similarity NPC477934
0.625 Remote Similarity NPC159789
0.625 Remote Similarity NPC478126
0.625 Remote Similarity NPC472021
0.6237 Remote Similarity NPC74466
0.6237 Remote Similarity NPC472273
0.6235 Remote Similarity NPC268578
0.6235 Remote Similarity NPC15091
0.6235 Remote Similarity NPC259173
0.6235 Remote Similarity NPC269684
0.6235 Remote Similarity NPC292458
0.6235 Remote Similarity NPC217559
0.6235 Remote Similarity NPC472847
0.6234 Remote Similarity NPC476734
0.6234 Remote Similarity NPC285003
0.6234 Remote Similarity NPC469941
0.6234 Remote Similarity NPC241265
0.6234 Remote Similarity NPC319671
0.6234 Remote Similarity NPC252032
0.6234 Remote Similarity NPC474962
0.6222 Remote Similarity NPC52756
0.622 Remote Similarity NPC185465
0.622 Remote Similarity NPC177343
0.622 Remote Similarity NPC80089
0.622 Remote Similarity NPC470014
0.622 Remote Similarity NPC26029
0.622 Remote Similarity NPC224802
0.622 Remote Similarity NPC272841
0.622 Remote Similarity NPC243594
0.622 Remote Similarity NPC34046
0.622 Remote Similarity NPC324700
0.622 Remote Similarity NPC478084
0.622 Remote Similarity NPC476732
0.622 Remote Similarity NPC199965
0.622 Remote Similarity NPC31031
0.622 Remote Similarity NPC476810
0.622 Remote Similarity NPC171426
0.6212 Remote Similarity NPC305182
0.6211 Remote Similarity NPC477172
0.6211 Remote Similarity NPC478181
0.6207 Remote Similarity NPC474215
0.6207 Remote Similarity NPC83242
0.6207 Remote Similarity NPC120395
0.6207 Remote Similarity NPC474062
0.6207 Remote Similarity NPC475729
0.6203 Remote Similarity NPC232112
0.6203 Remote Similarity NPC474123
0.6203 Remote Similarity NPC248567
0.6203 Remote Similarity NPC475260
0.6203 Remote Similarity NPC475232
0.6203 Remote Similarity NPC475230

  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 NPC473899 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
0.6835 Remote Similarity NPD4238 Approved
0.6835 Remote Similarity NPD4802 Phase 2
0.6818 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6806 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6667 Remote Similarity NPD2257 Approved
0.6567 Remote Similarity NPD615 Clinical (unspecified phase)
0.6456 Remote Similarity NPD3702 Approved
0.6447 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6447 Remote Similarity NPD3700 Clinical (unspecified phase)
0.6447 Remote Similarity NPD3698 Phase 2
0.6438 Remote Similarity NPD7909 Approved
0.6406 Remote Similarity NPD2266 Phase 2
0.6364 Remote Similarity NPD4789 Approved
0.6364 Remote Similarity NPD4244 Approved
0.6364 Remote Similarity NPD4245 Approved
0.6349 Remote Similarity NPD634 Phase 3
0.6338 Remote Similarity NPD3198 Approved
0.6282 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6282 Remote Similarity NPD4808 Clinical (unspecified phase)
0.6269 Remote Similarity NPD3186 Phase 1
0.6267 Remote Similarity NPD4224 Phase 2
0.625 Remote Similarity NPD3703 Phase 2
0.622 Remote Similarity NPD6115 Approved
0.622 Remote Similarity NPD6118 Approved
0.622 Remote Similarity NPD6697 Approved
0.622 Remote Similarity NPD6114 Approved
0.619 Remote Similarity NPD1780 Approved
0.619 Remote Similarity NPD1779 Approved
0.6173 Remote Similarity NPD6117 Approved
0.6125 Remote Similarity NPD1810 Approved
0.6125 Remote Similarity NPD1811 Approved
0.6125 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6098 Remote Similarity NPD6116 Phase 1
0.6076 Remote Similarity NPD6081 Approved
0.6076 Remote Similarity NPD5777 Approved
0.6047 Remote Similarity NPD3669 Approved
0.6047 Remote Similarity NPD3670 Clinical (unspecified phase)
0.602 Remote Similarity NPD8170 Clinical (unspecified phase)
0.59 Remote Similarity NPD6412 Phase 2
0.5897 Remote Similarity NPD5360 Phase 3
0.5897 Remote Similarity NPD5361 Clinical (unspecified phase)
0.5873 Remote Similarity NPD387 Clinical (unspecified phase)
0.5857 Remote Similarity NPD3730 Approved
0.5857 Remote Similarity NPD3728 Approved
0.5833 Remote Similarity NPD3671 Phase 1
0.5784 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5758 Remote Similarity NPD384 Approved
0.5758 Remote Similarity NPD385 Approved
0.5699 Remote Similarity NPD6411 Approved
0.5696 Remote Similarity NPD229 Approved
0.5686 Remote Similarity NPD6686 Approved
0.5679 Remote Similarity NPD4758 Discontinued
0.5657 Remote Similarity NPD8082 Approved
0.5657 Remote Similarity NPD8138 Approved
0.5657 Remote Similarity NPD8085 Approved
0.5657 Remote Similarity NPD8139 Approved
0.5657 Remote Similarity NPD8084 Approved
0.5657 Remote Similarity NPD8083 Approved
0.5657 Remote Similarity NPD8086 Approved
0.5652 Remote Similarity NPD9638 Phase 2
0.5647 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5625 Remote Similarity NPD3726 Approved
0.5625 Remote Similarity NPD3725 Approved
0.5606 Remote Similarity NPD386 Approved
0.5606 Remote Similarity NPD388 Approved
0.56 Remote Similarity NPD8276 Approved
0.56 Remote Similarity NPD8275 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