Structure

Physi-Chem Properties

Molecular Weight:  258.18
Volume:  274.668
LogP:  3.866
LogD:  3.114
LogS:  -3.035
# Rotatable Bonds:  7
TPSA:  55.76
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.709
Synthetic Accessibility Score:  4.147
Fsp3:  0.929
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.67
MDCK Permeability:  3.592683424358256e-05
Pgp-inhibitor:  0.099
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.13
Plasma Protein Binding (PPB):  91.46968078613281%
Volume Distribution (VD):  0.27
Pgp-substrate:  8.84178352355957%

ADMET: Metabolism

CYP1A2-inhibitor:  0.034
CYP1A2-substrate:  0.759
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.904
CYP2C9-inhibitor:  0.073
CYP2C9-substrate:  0.859
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.212
CYP3A4-inhibitor:  0.085
CYP3A4-substrate:  0.129

ADMET: Excretion

Clearance (CL):  10.688
Half-life (T1/2):  0.745

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.414
Drug-inuced Liver Injury (DILI):  0.066
AMES Toxicity:  0.024
Rat Oral Acute Toxicity:  0.077
Maximum Recommended Daily Dose:  0.2
Skin Sensitization:  0.449
Carcinogencity:  0.397
Eye Corrosion:  0.942
Eye Irritation:  0.953
Respiratory Toxicity:  0.954

Download Data

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

  Natural Product: NPC475821

Natural Product ID:  NPC475821
Common Name*:   2-[(3S,4R)-6-Butyl-4,6-Diethyldioxan-3-Yl]Acetic Acid
IUPAC Name:   2-[(3S,4R)-6-butyl-4,6-diethyldioxan-3-yl]acetic acid
Synonyms:  
Standard InCHIKey:  XVBNSADIMCHWSG-RJTITELWSA-N
Standard InCHI:  InChI=1S/C14H26O4/c1-4-7-8-14(6-3)10-11(5-2)12(17-18-14)9-13(15)16/h11-12H,4-10H2,1-3H3,(H,15,16)/t11-,12+,14?/m1/s1
SMILES:  CCCCC1(CC)OO[C@H]([C@@H](C1)CC)CC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL516729
PubChem CID:   10264495
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000368] Dioxanes
        • [CHEMONTID:0001312] 1,2-dioxanes

*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
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. red sea n.a. PMID[12762806]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[18027906]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[22469701]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. collected by hand at a depth of 10 m off the shore of Iriomote Island, Okinawa Prefecture, Japan 2009-JUN PMID[23855338]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[24948562]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[27015002]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. New Guinea n.a. PMID[8158156]

☑ 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
NPT168 Cell Line P388 Mus musculus ED50 = 2.6 ug ml-1 PMID[560278]

☑ 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 NPC475821 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
0.9483 High Similarity NPC474552
0.8966 High Similarity NPC472019
0.8966 High Similarity NPC472020
0.8966 High Similarity NPC226602
0.8814 High Similarity NPC472021
0.8254 Intermediate Similarity NPC476330
0.8254 Intermediate Similarity NPC215987
0.8254 Intermediate Similarity NPC306805
0.7969 Intermediate Similarity NPC469926
0.7857 Intermediate Similarity NPC469514
0.7746 Intermediate Similarity NPC281296
0.7746 Intermediate Similarity NPC122847
0.7742 Intermediate Similarity NPC469924
0.7727 Intermediate Similarity NPC469925
0.7714 Intermediate Similarity NPC60718
0.7679 Intermediate Similarity NPC131770
0.7679 Intermediate Similarity NPC200618
0.7639 Intermediate Similarity NPC476986
0.7639 Intermediate Similarity NPC470905
0.7639 Intermediate Similarity NPC121200
0.7636 Intermediate Similarity NPC314679
0.7619 Intermediate Similarity NPC469921
0.7538 Intermediate Similarity NPC314103
0.7534 Intermediate Similarity NPC82488
0.7534 Intermediate Similarity NPC308545
0.7534 Intermediate Similarity NPC113363
0.75 Intermediate Similarity NPC469923
0.75 Intermediate Similarity NPC474003
0.746 Intermediate Similarity NPC470363
0.7455 Intermediate Similarity NPC55023
0.7429 Intermediate Similarity NPC167145
0.7414 Intermediate Similarity NPC90904
0.7368 Intermediate Similarity NPC324793
0.7368 Intermediate Similarity NPC477878
0.7333 Intermediate Similarity NPC72722
0.7333 Intermediate Similarity NPC117960
0.7333 Intermediate Similarity NPC172309
0.7333 Intermediate Similarity NPC14044
0.7324 Intermediate Similarity NPC330016
0.7313 Intermediate Similarity NPC241949
0.726 Intermediate Similarity NPC469867
0.7237 Intermediate Similarity NPC475395
0.7237 Intermediate Similarity NPC476984
0.7237 Intermediate Similarity NPC476292
0.7237 Intermediate Similarity NPC474605
0.7222 Intermediate Similarity NPC199445
0.7193 Intermediate Similarity NPC21844
0.7143 Intermediate Similarity NPC476983
0.7143 Intermediate Similarity NPC476100
0.7123 Intermediate Similarity NPC474447
0.7123 Intermediate Similarity NPC152754
0.7123 Intermediate Similarity NPC476985
0.7123 Intermediate Similarity NPC59602
0.7123 Intermediate Similarity NPC474316
0.7123 Intermediate Similarity NPC475744
0.7123 Intermediate Similarity NPC476987
0.7121 Intermediate Similarity NPC235788
0.7101 Intermediate Similarity NPC319007
0.7083 Intermediate Similarity NPC477867
0.7051 Intermediate Similarity NPC471343
0.7042 Intermediate Similarity NPC96322
0.7027 Intermediate Similarity NPC476325
0.7027 Intermediate Similarity NPC476264
0.7027 Intermediate Similarity NPC83108
0.7027 Intermediate Similarity NPC214030
0.7 Intermediate Similarity NPC98711
0.7 Intermediate Similarity NPC314084
0.6986 Remote Similarity NPC179922
0.6986 Remote Similarity NPC255060
0.697 Remote Similarity NPC469922
0.6962 Remote Similarity NPC471344
0.6923 Remote Similarity NPC69469
0.6923 Remote Similarity NPC17935
0.6909 Remote Similarity NPC248763
0.6909 Remote Similarity NPC325452
0.6897 Remote Similarity NPC328497
0.6897 Remote Similarity NPC324004
0.6892 Remote Similarity NPC266119
0.6892 Remote Similarity NPC474020
0.6892 Remote Similarity NPC239127
0.6875 Remote Similarity NPC476982
0.6875 Remote Similarity NPC262085
0.6875 Remote Similarity NPC476104
0.6875 Remote Similarity NPC475181
0.6849 Remote Similarity NPC317212
0.6842 Remote Similarity NPC268502
0.6842 Remote Similarity NPC254996
0.6833 Remote Similarity NPC305182
0.6806 Remote Similarity NPC474590
0.6806 Remote Similarity NPC126061
0.68 Remote Similarity NPC307865
0.678 Remote Similarity NPC13105
0.678 Remote Similarity NPC106872
0.6761 Remote Similarity NPC475062
0.6757 Remote Similarity NPC228411
0.6753 Remote Similarity NPC274522
0.6753 Remote Similarity NPC476265
0.6724 Remote Similarity NPC133771
0.6714 Remote Similarity NPC286842
0.6712 Remote Similarity NPC474755
0.6712 Remote Similarity NPC238425
0.6712 Remote Similarity NPC474543
0.6712 Remote Similarity NPC472018
0.6667 Remote Similarity NPC475481
0.6667 Remote Similarity NPC304162
0.6667 Remote Similarity NPC470268
0.6667 Remote Similarity NPC53463
0.6667 Remote Similarity NPC76051
0.6667 Remote Similarity NPC469937
0.6667 Remote Similarity NPC69462
0.6667 Remote Similarity NPC23155
0.6667 Remote Similarity NPC476988
0.6667 Remote Similarity NPC320588
0.6667 Remote Similarity NPC79277
0.6627 Remote Similarity NPC471342
0.6627 Remote Similarity NPC469866
0.6623 Remote Similarity NPC19841
0.6622 Remote Similarity NPC474551
0.6622 Remote Similarity NPC215030
0.6622 Remote Similarity NPC477930
0.662 Remote Similarity NPC82315
0.661 Remote Similarity NPC326957
0.661 Remote Similarity NPC249754
0.6585 Remote Similarity NPC51662
0.6585 Remote Similarity NPC314364
0.6579 Remote Similarity NPC70996
0.6579 Remote Similarity NPC477918
0.6575 Remote Similarity NPC478227
0.6575 Remote Similarity NPC470243
0.6571 Remote Similarity NPC473899
0.6571 Remote Similarity NPC315525
0.6571 Remote Similarity NPC135043
0.6545 Remote Similarity NPC279026
0.6545 Remote Similarity NPC118968
0.6545 Remote Similarity NPC301696
0.6545 Remote Similarity NPC183424
0.6545 Remote Similarity NPC154186
0.6545 Remote Similarity NPC294085
0.6545 Remote Similarity NPC214610
0.6545 Remote Similarity NPC3531
0.6545 Remote Similarity NPC201844
0.6545 Remote Similarity NPC301585
0.6545 Remote Similarity NPC14227
0.6545 Remote Similarity NPC261080
0.6545 Remote Similarity NPC113928
0.6543 Remote Similarity NPC477205
0.6538 Remote Similarity NPC469920
0.6533 Remote Similarity NPC477934
0.6533 Remote Similarity NPC132064
0.6533 Remote Similarity NPC68565
0.6533 Remote Similarity NPC35871
0.6528 Remote Similarity NPC28526
0.6528 Remote Similarity NPC107130
0.6494 Remote Similarity NPC470014
0.6479 Remote Similarity NPC41542
0.6463 Remote Similarity NPC476717
0.6463 Remote Similarity NPC477994
0.6463 Remote Similarity NPC477993
0.6452 Remote Similarity NPC100096
0.6447 Remote Similarity NPC477933
0.6447 Remote Similarity NPC477932
0.6441 Remote Similarity NPC308301
0.6441 Remote Similarity NPC12438
0.6441 Remote Similarity NPC30195
0.6429 Remote Similarity NPC295256
0.6429 Remote Similarity NPC19311
0.6429 Remote Similarity NPC230047
0.6429 Remote Similarity NPC469791
0.642 Remote Similarity NPC120158
0.642 Remote Similarity NPC477434
0.642 Remote Similarity NPC475193
0.641 Remote Similarity NPC474754
0.641 Remote Similarity NPC246458
0.6406 Remote Similarity NPC319589
0.64 Remote Similarity NPC48641
0.6389 Remote Similarity NPC119838
0.6379 Remote Similarity NPC74845
0.6377 Remote Similarity NPC325773
0.6375 Remote Similarity NPC477936
0.6375 Remote Similarity NPC477935
0.6364 Remote Similarity NPC207010
0.6364 Remote Similarity NPC317913
0.6364 Remote Similarity NPC108014
0.6364 Remote Similarity NPC474433
0.6364 Remote Similarity NPC268826
0.6364 Remote Similarity NPC169389
0.6351 Remote Similarity NPC185419
0.6351 Remote Similarity NPC184550
0.6341 Remote Similarity NPC131350
0.6341 Remote Similarity NPC478111
0.6329 Remote Similarity NPC103634
0.6316 Remote Similarity NPC196924
0.6316 Remote Similarity NPC209970
0.6316 Remote Similarity NPC171736
0.6316 Remote Similarity NPC149184
0.6316 Remote Similarity NPC307783
0.6316 Remote Similarity NPC216630
0.6316 Remote Similarity NPC53541
0.631 Remote Similarity NPC471221
0.6296 Remote Similarity NPC472847

  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 NPC475821 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
0.7636 Intermediate Similarity NPD634 Phase 3
0.75 Intermediate Similarity NPD3729 Clinical (unspecified phase)
0.7213 Intermediate Similarity NPD615 Clinical (unspecified phase)
0.7188 Intermediate Similarity NPD3198 Approved
0.7015 Intermediate Similarity NPD7909 Approved
0.7 Intermediate Similarity NPD9638 Phase 2
0.6885 Remote Similarity NPD3186 Phase 1
0.6711 Remote Similarity NPD4238 Approved
0.6711 Remote Similarity NPD4802 Phase 2
0.6667 Remote Similarity NPD3730 Approved
0.6667 Remote Similarity NPD3728 Approved
0.6545 Remote Similarity NPD633 Phase 3
0.6545 Remote Similarity NPD9655 Approved
0.6545 Remote Similarity NPD9450 Approved
0.6545 Remote Similarity NPD77 Approved
0.6545 Remote Similarity NPD9448 Phase 2
0.6491 Remote Similarity NPD387 Clinical (unspecified phase)
0.6429 Remote Similarity NPD9496 Clinical (unspecified phase)
0.6389 Remote Similarity NPD229 Approved
0.6364 Remote Similarity NPD6116 Phase 1
0.6316 Remote Similarity NPD3702 Approved
0.6316 Remote Similarity NPD2270 Approved
0.6271 Remote Similarity NPD2699 Approved
0.625 Remote Similarity NPD5369 Approved
0.6234 Remote Similarity NPD6117 Approved
0.623 Remote Similarity NPD6125 Clinical (unspecified phase)
0.623 Remote Similarity NPD2266 Phase 2
0.6212 Remote Similarity NPD73 Approved
0.6184 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6182 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6125 Remote Similarity NPD5368 Approved
0.6111 Remote Similarity NPD4224 Phase 2
0.6076 Remote Similarity NPD6118 Approved
0.6076 Remote Similarity NPD6114 Approved
0.6076 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6076 Remote Similarity NPD7917 Clinical (unspecified phase)
0.6076 Remote Similarity NPD6697 Approved
0.6076 Remote Similarity NPD6115 Approved
0.6047 Remote Similarity NPD5764 Clinical (unspecified phase)
0.6047 Remote Similarity NPD6101 Approved
0.6 Remote Similarity NPD3199 Clinical (unspecified phase)
0.5976 Remote Similarity NPD4269 Approved
0.5976 Remote Similarity NPD4270 Approved
0.5976 Remote Similarity NPD7345 Approved
0.5976 Remote Similarity NPD6435 Approved
0.5972 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5932 Remote Similarity NPD1462 Approved
0.5926 Remote Similarity NPD4820 Approved
0.5926 Remote Similarity NPD4822 Approved
0.5926 Remote Similarity NPD4819 Approved
0.5926 Remote Similarity NPD4821 Approved
0.5921 Remote Similarity NPD6081 Approved
0.5909 Remote Similarity NPD6411 Approved
0.5897 Remote Similarity NPD2257 Approved
0.5882 Remote Similarity NPD8959 Approved
0.5867 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5867 Remote Similarity NPD3698 Phase 2
0.5867 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5862 Remote Similarity NPD9635 Discontinued
0.5862 Remote Similarity NPD1460 Approved
0.5857 Remote Similarity NPD9656 Approved
0.5854 Remote Similarity NPD1779 Approved
0.5854 Remote Similarity NPD1780 Approved
0.5846 Remote Similarity NPD9008 Approved
0.5846 Remote Similarity NPD9011 Approved
0.5846 Remote Similarity NPD8960 Approved
0.5846 Remote Similarity NPD64 Approved
0.5846 Remote Similarity NPD9010 Approved
0.5846 Remote Similarity NPD72 Approved
0.5846 Remote Similarity NPD65 Approved
0.5846 Remote Similarity NPD9007 Approved
0.5846 Remote Similarity NPD66 Approved
0.5846 Remote Similarity NPD9009 Approved
0.5818 Remote Similarity NPD9447 Approved
0.5806 Remote Similarity NPD385 Approved
0.5806 Remote Similarity NPD384 Approved
0.5795 Remote Similarity NPD46 Approved
0.5795 Remote Similarity NPD6698 Approved
0.5789 Remote Similarity NPD3206 Approved
0.5789 Remote Similarity NPD4245 Approved
0.5789 Remote Similarity NPD4244 Approved
0.5775 Remote Similarity NPD9676 Phase 3
0.5765 Remote Similarity NPD5363 Approved
0.5753 Remote Similarity NPD7341 Phase 2
0.5732 Remote Similarity NPD4252 Approved
0.573 Remote Similarity NPD7983 Approved
0.5714 Remote Similarity NPD5777 Approved
0.5714 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3670 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3669 Approved
0.5714 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7154 Phase 3
0.5698 Remote Similarity NPD5786 Approved
0.5684 Remote Similarity NPD8138 Approved
0.5684 Remote Similarity NPD8083 Approved
0.5684 Remote Similarity NPD8139 Approved
0.5684 Remote Similarity NPD8086 Approved
0.5684 Remote Similarity NPD8085 Approved
0.5684 Remote Similarity NPD8082 Approved
0.5684 Remote Similarity NPD8084 Approved
0.5679 Remote Similarity NPD4271 Approved
0.5679 Remote Similarity NPD4268 Approved
0.5679 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5667 Remote Similarity NPD5779 Approved
0.5667 Remote Similarity NPD5778 Approved
0.5652 Remote Similarity NPD9439 Approved
0.5652 Remote Similarity NPD7839 Suspended
0.5652 Remote Similarity NPD9438 Approved
0.5645 Remote Similarity NPD386 Approved
0.5645 Remote Similarity NPD388 Approved
0.5625 Remote Similarity NPD9129 Approved
0.5625 Remote Similarity NPD8276 Approved
0.5625 Remote Similarity NPD71 Approved
0.5625 Remote Similarity NPD9126 Approved
0.5625 Remote Similarity NPD8275 Approved
0.5616 Remote Similarity NPD371 Approved
0.5604 Remote Similarity NPD5282 Discontinued
0.56 Remote Similarity NPD897 Approved
0.56 Remote Similarity NPD898 Approved
0.56 Remote Similarity NPD896 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