Structure

Physi-Chem Properties

Molecular Weight:  224.1
Volume:  226.247
LogP:  1.174
LogD:  0.94
LogS:  -3.111
# Rotatable Bonds:  4
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.68
Synthetic Accessibility Score:  4.089
Fsp3:  0.667
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:  -4.725
MDCK Permeability:  3.121849294984713e-05
Pgp-inhibitor:  0.902
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.074
30% Bioavailability (F30%):  0.042

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.989
Plasma Protein Binding (PPB):  50.21312713623047%
Volume Distribution (VD):  0.654
Pgp-substrate:  58.35896682739258%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.299
CYP2C19-inhibitor:  0.048
CYP2C19-substrate:  0.613
CYP2C9-inhibitor:  0.027
CYP2C9-substrate:  0.063
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.074
CYP3A4-inhibitor:  0.085
CYP3A4-substrate:  0.422

ADMET: Excretion

Clearance (CL):  8.447
Half-life (T1/2):  0.907

ADMET: Toxicity

hERG Blockers:  0.055
Human Hepatotoxicity (H-HT):  0.182
Drug-inuced Liver Injury (DILI):  0.209
AMES Toxicity:  0.9
Rat Oral Acute Toxicity:  0.806
Maximum Recommended Daily Dose:  0.899
Skin Sensitization:  0.954
Carcinogencity:  0.844
Eye Corrosion:  0.023
Eye Irritation:  0.183
Respiratory Toxicity:  0.604

Download Data

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

  Natural Product: NPC473980

Natural Product ID:  NPC473980
Common Name*:   (3Ar,7Ar)-6-Oxo-2,3,3A,6,7,7A-Hexahydrobenzofuran-3A-Yl Butyrate
IUPAC Name:   [(3aR,7aR)-6-oxo-2,3,7,7a-tetrahydro-1-benzofuran-3a-yl] butanoate
Synonyms:  
Standard InCHIKey:  JAVHUWBEBUGAOD-PWSUYJOCSA-N
Standard InCHI:  InChI=1S/C12H16O4/c1-2-3-11(14)16-12-5-4-9(13)8-10(12)15-7-6-12/h4-5,10H,2-3,6-8H2,1H3/t10-,12+/m1/s1
SMILES:  CCCC(=O)O[C@]12CCO[C@@H]2CC(=O)C=C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL457080
PubChem CID:   44567068
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000301] Benzofurans

*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
NPO33459 cornus controversa Species Cornaceae Eukaryota n.a. n.a. n.a. PMID[3236014]

☑ 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 IC50 = 0.6 ug.mL-1 PMID[507650]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 2.7 ug.mL-1 PMID[507650]

☑ 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 NPC473980 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
1.0 High Similarity NPC473981
0.9863 High Similarity NPC475699
0.9605 High Similarity NPC475690
0.8333 Intermediate Similarity NPC474197
0.825 Intermediate Similarity NPC475210
0.8077 Intermediate Similarity NPC476355
0.8072 Intermediate Similarity NPC475947
0.8049 Intermediate Similarity NPC275507
0.8025 Intermediate Similarity NPC270126
0.8 Intermediate Similarity NPC474278
0.8 Intermediate Similarity NPC41780
0.8 Intermediate Similarity NPC187568
0.7952 Intermediate Similarity NPC474252
0.7907 Intermediate Similarity NPC266957
0.7907 Intermediate Similarity NPC72513
0.7882 Intermediate Similarity NPC155873
0.7875 Intermediate Similarity NPC123360
0.7865 Intermediate Similarity NPC165383
0.7848 Intermediate Similarity NPC140287
0.7821 Intermediate Similarity NPC163003
0.7805 Intermediate Similarity NPC178277
0.7778 Intermediate Similarity NPC476028
0.7778 Intermediate Similarity NPC141789
0.7778 Intermediate Similarity NPC97516
0.7778 Intermediate Similarity NPC171204
0.7765 Intermediate Similarity NPC163615
0.7765 Intermediate Similarity NPC38569
0.7753 Intermediate Similarity NPC261607
0.7753 Intermediate Similarity NPC300312
0.7753 Intermediate Similarity NPC111114
0.7727 Intermediate Similarity NPC78008
0.7722 Intermediate Similarity NPC295633
0.7722 Intermediate Similarity NPC269206
0.7722 Intermediate Similarity NPC58956
0.7717 Intermediate Similarity NPC266842
0.7711 Intermediate Similarity NPC281132
0.7711 Intermediate Similarity NPC223904
0.7683 Intermediate Similarity NPC267231
0.7683 Intermediate Similarity NPC108816
0.7683 Intermediate Similarity NPC93763
0.7674 Intermediate Similarity NPC470755
0.7667 Intermediate Similarity NPC469692
0.7667 Intermediate Similarity NPC469645
0.7662 Intermediate Similarity NPC470256
0.7647 Intermediate Similarity NPC318468
0.7647 Intermediate Similarity NPC170286
0.7625 Intermediate Similarity NPC474280
0.7619 Intermediate Similarity NPC141810
0.7619 Intermediate Similarity NPC297440
0.7619 Intermediate Similarity NPC471325
0.7619 Intermediate Similarity NPC281949
0.7619 Intermediate Similarity NPC25684
0.7619 Intermediate Similarity NPC301477
0.7614 Intermediate Similarity NPC153570
0.759 Intermediate Similarity NPC472965
0.759 Intermediate Similarity NPC63649
0.759 Intermediate Similarity NPC264227
0.7586 Intermediate Similarity NPC38576
0.7586 Intermediate Similarity NPC279859
0.7586 Intermediate Similarity NPC469483
0.7586 Intermediate Similarity NPC478112
0.7586 Intermediate Similarity NPC469910
0.7582 Intermediate Similarity NPC167219
0.7582 Intermediate Similarity NPC121825
0.7564 Intermediate Similarity NPC476591
0.7564 Intermediate Similarity NPC88877
0.7561 Intermediate Similarity NPC65603
0.7561 Intermediate Similarity NPC57744
0.7558 Intermediate Similarity NPC158756
0.7532 Intermediate Similarity NPC194871
0.7531 Intermediate Similarity NPC138408
0.7531 Intermediate Similarity NPC155587
0.7531 Intermediate Similarity NPC193351
0.7531 Intermediate Similarity NPC226669
0.7529 Intermediate Similarity NPC173609
0.7529 Intermediate Similarity NPC85772
0.75 Intermediate Similarity NPC287878
0.75 Intermediate Similarity NPC469920
0.75 Intermediate Similarity NPC472007
0.75 Intermediate Similarity NPC473248
0.7474 Intermediate Similarity NPC474742
0.7471 Intermediate Similarity NPC215364
0.7471 Intermediate Similarity NPC125290
0.7471 Intermediate Similarity NPC21471
0.7471 Intermediate Similarity NPC473353
0.7471 Intermediate Similarity NPC177932
0.7471 Intermediate Similarity NPC33570
0.747 Intermediate Similarity NPC128276
0.7444 Intermediate Similarity NPC144133
0.7444 Intermediate Similarity NPC49342
0.7444 Intermediate Similarity NPC251385
0.7444 Intermediate Similarity NPC51653
0.7444 Intermediate Similarity NPC474232
0.7444 Intermediate Similarity NPC473455
0.7444 Intermediate Similarity NPC179394
0.7442 Intermediate Similarity NPC169575
0.7442 Intermediate Similarity NPC59097
0.7442 Intermediate Similarity NPC40746
0.7439 Intermediate Similarity NPC235906
0.7419 Intermediate Similarity NPC17585
0.7416 Intermediate Similarity NPC475902
0.7416 Intermediate Similarity NPC469653
0.7416 Intermediate Similarity NPC475906
0.7416 Intermediate Similarity NPC476803
0.7416 Intermediate Similarity NPC475819
0.7416 Intermediate Similarity NPC476805
0.7416 Intermediate Similarity NPC471047
0.7416 Intermediate Similarity NPC469628
0.7416 Intermediate Similarity NPC469631
0.7412 Intermediate Similarity NPC24417
0.7412 Intermediate Similarity NPC42470
0.7407 Intermediate Similarity NPC117746
0.7407 Intermediate Similarity NPC15499
0.7407 Intermediate Similarity NPC474758
0.7407 Intermediate Similarity NPC294434
0.7407 Intermediate Similarity NPC259599
0.7396 Intermediate Similarity NPC149371
0.7391 Intermediate Similarity NPC471147
0.7386 Intermediate Similarity NPC472009
0.7386 Intermediate Similarity NPC107787
0.7381 Intermediate Similarity NPC167881
0.7381 Intermediate Similarity NPC98557
0.7381 Intermediate Similarity NPC471299
0.7381 Intermediate Similarity NPC99651
0.7381 Intermediate Similarity NPC617
0.7381 Intermediate Similarity NPC150646
0.7368 Intermediate Similarity NPC477512
0.7363 Intermediate Similarity NPC284185
0.7363 Intermediate Similarity NPC150978
0.7363 Intermediate Similarity NPC32944
0.7363 Intermediate Similarity NPC70595
0.7363 Intermediate Similarity NPC74103
0.7363 Intermediate Similarity NPC123177
0.7363 Intermediate Similarity NPC193396
0.7356 Intermediate Similarity NPC159635
0.7356 Intermediate Similarity NPC41856
0.7356 Intermediate Similarity NPC115786
0.7356 Intermediate Similarity NPC96259
0.7356 Intermediate Similarity NPC141193
0.7349 Intermediate Similarity NPC7563
0.7349 Intermediate Similarity NPC320630
0.7349 Intermediate Similarity NPC476794
0.7349 Intermediate Similarity NPC116177
0.7349 Intermediate Similarity NPC470240
0.7349 Intermediate Similarity NPC474760
0.7342 Intermediate Similarity NPC199557
0.7333 Intermediate Similarity NPC87306
0.7326 Intermediate Similarity NPC229825
0.7326 Intermediate Similarity NPC26624
0.732 Intermediate Similarity NPC475871
0.732 Intermediate Similarity NPC475945
0.7312 Intermediate Similarity NPC214694
0.7312 Intermediate Similarity NPC471142
0.7312 Intermediate Similarity NPC475659
0.7312 Intermediate Similarity NPC477922
0.7308 Intermediate Similarity NPC203335
0.7303 Intermediate Similarity NPC231889
0.7303 Intermediate Similarity NPC300779
0.7303 Intermediate Similarity NPC23622
0.7303 Intermediate Similarity NPC160138
0.7294 Intermediate Similarity NPC302426
0.7292 Intermediate Similarity NPC47880
0.7292 Intermediate Similarity NPC164598
0.7292 Intermediate Similarity NPC46998
0.7292 Intermediate Similarity NPC128733
0.7292 Intermediate Similarity NPC185141
0.7292 Intermediate Similarity NPC133907
0.7292 Intermediate Similarity NPC474339
0.7292 Intermediate Similarity NPC110443
0.7284 Intermediate Similarity NPC472956
0.7283 Intermediate Similarity NPC295204
0.7283 Intermediate Similarity NPC162205
0.7283 Intermediate Similarity NPC273579
0.7283 Intermediate Similarity NPC288240
0.7273 Intermediate Similarity NPC21469
0.7273 Intermediate Similarity NPC261380
0.7273 Intermediate Similarity NPC50362
0.7273 Intermediate Similarity NPC78089
0.7273 Intermediate Similarity NPC165162
0.7273 Intermediate Similarity NPC11804
0.7273 Intermediate Similarity NPC319795
0.7273 Intermediate Similarity NPC38468
0.7263 Intermediate Similarity NPC471144
0.7263 Intermediate Similarity NPC208233
0.7262 Intermediate Similarity NPC196653
0.7262 Intermediate Similarity NPC471465
0.7253 Intermediate Similarity NPC62815
0.7253 Intermediate Similarity NPC473619
0.7253 Intermediate Similarity NPC253144
0.7253 Intermediate Similarity NPC475748
0.7253 Intermediate Similarity NPC166554
0.7253 Intermediate Similarity NPC475855
0.725 Intermediate Similarity NPC472017
0.725 Intermediate Similarity NPC69462
0.7245 Intermediate Similarity NPC146731
0.7245 Intermediate Similarity NPC296950
0.7245 Intermediate Similarity NPC474741
0.7241 Intermediate Similarity NPC473390
0.7241 Intermediate Similarity NPC39588
0.7241 Intermediate Similarity NPC250315

  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 NPC473980 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
0.7471 Intermediate Similarity NPD1694 Approved
0.7273 Intermediate Similarity NPD1733 Clinical (unspecified phase)
0.7128 Intermediate Similarity NPD1698 Clinical (unspecified phase)
0.7126 Intermediate Similarity NPD5209 Approved
0.7065 Intermediate Similarity NPD5785 Approved
0.6907 Remote Similarity NPD4225 Approved
0.6889 Remote Similarity NPD5363 Approved
0.6765 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6702 Remote Similarity NPD6698 Approved
0.6702 Remote Similarity NPD46 Approved
0.6667 Remote Similarity NPD7115 Discovery
0.6629 Remote Similarity NPD5369 Approved
0.6625 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6596 Remote Similarity NPD1695 Approved
0.6571 Remote Similarity NPD6371 Approved
0.6556 Remote Similarity NPD4269 Approved
0.6556 Remote Similarity NPD4270 Approved
0.6556 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6517 Remote Similarity NPD4252 Approved
0.6512 Remote Similarity NPD8039 Approved
0.6452 Remote Similarity NPD5786 Approved
0.64 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6354 Remote Similarity NPD7838 Discovery
0.6333 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6327 Remote Similarity NPD5282 Discontinued
0.6304 Remote Similarity NPD7154 Phase 3
0.6289 Remote Similarity NPD4810 Clinical (unspecified phase)
0.6289 Remote Similarity NPD7983 Approved
0.625 Remote Similarity NPD5370 Suspended
0.6224 Remote Similarity NPD5779 Approved
0.6224 Remote Similarity NPD5778 Approved
0.618 Remote Similarity NPD4756 Discovery
0.6154 Remote Similarity NPD4820 Approved
0.6154 Remote Similarity NPD4819 Approved
0.6154 Remote Similarity NPD4822 Approved
0.6154 Remote Similarity NPD4821 Approved
0.6111 Remote Similarity NPD4268 Approved
0.6111 Remote Similarity NPD4271 Approved
0.6105 Remote Similarity NPD4249 Approved
0.6082 Remote Similarity NPD6101 Approved
0.6082 Remote Similarity NPD5764 Clinical (unspecified phase)
0.6064 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6055 Remote Similarity NPD8413 Clinical (unspecified phase)
0.6042 Remote Similarity NPD4251 Approved
0.6042 Remote Similarity NPD4250 Approved
0.6034 Remote Similarity NPD7642 Approved
0.6022 Remote Similarity NPD6435 Approved
0.6019 Remote Similarity NPD6648 Approved
0.6 Remote Similarity NPD8516 Approved
0.6 Remote Similarity NPD8515 Approved
0.6 Remote Similarity NPD8517 Approved
0.6 Remote Similarity NPD8513 Phase 3
0.5981 Remote Similarity NPD5954 Clinical (unspecified phase)
0.5963 Remote Similarity NPD2067 Discontinued
0.5962 Remote Similarity NPD5344 Discontinued
0.596 Remote Similarity NPD5693 Phase 1
0.596 Remote Similarity NPD6411 Approved
0.5957 Remote Similarity NPD5362 Discontinued
0.5952 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5938 Remote Similarity NPD7146 Approved
0.5938 Remote Similarity NPD7521 Approved
0.5938 Remote Similarity NPD6409 Approved
0.5938 Remote Similarity NPD6684 Approved
0.5938 Remote Similarity NPD7334 Approved
0.5938 Remote Similarity NPD5330 Approved
0.5934 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5926 Remote Similarity NPD6686 Approved
0.5882 Remote Similarity NPD7839 Suspended
0.5859 Remote Similarity NPD5207 Approved
0.5833 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5818 Remote Similarity NPD5955 Clinical (unspecified phase)
0.5816 Remote Similarity NPD5737 Approved
0.5816 Remote Similarity NPD6672 Approved
0.5816 Remote Similarity NPD6903 Approved
0.5816 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5806 Remote Similarity NPD5368 Approved
0.58 Remote Similarity NPD7637 Suspended
0.5789 Remote Similarity NPD6110 Phase 1
0.5784 Remote Similarity NPD6356 Clinical (unspecified phase)
0.5784 Remote Similarity NPD5695 Phase 3
0.5783 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5769 Remote Similarity NPD5696 Approved
0.5766 Remote Similarity NPD2181 Clinical (unspecified phase)
0.5765 Remote Similarity NPD7331 Phase 2
0.575 Remote Similarity NPD8074 Phase 3
0.5743 Remote Similarity NPD6399 Phase 3
0.5741 Remote Similarity NPD6008 Approved
0.5727 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6053 Discontinued
0.5714 Remote Similarity NPD8297 Approved
0.5714 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3573 Approved
0.5688 Remote Similarity NPD5697 Approved
0.5686 Remote Similarity NPD7900 Approved
0.5686 Remote Similarity NPD7901 Clinical (unspecified phase)
0.5673 Remote Similarity NPD6084 Phase 2
0.5673 Remote Similarity NPD6083 Phase 2
0.567 Remote Similarity NPD1696 Phase 3
0.5652 Remote Similarity NPD7500 Approved
0.5644 Remote Similarity NPD5694 Approved
0.5641 Remote Similarity NPD6319 Approved
0.5636 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5636 Remote Similarity NPD6899 Approved
0.5636 Remote Similarity NPD6881 Approved
0.563 Remote Similarity NPD7829 Approved
0.563 Remote Similarity NPD7830 Approved
0.5625 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6650 Approved
0.5625 Remote Similarity NPD6649 Approved
0.5625 Remote Similarity NPD5332 Approved
0.5625 Remote Similarity NPD5331 Approved
0.5625 Remote Similarity NPD2204 Approved
0.5619 Remote Similarity NPD7638 Approved
0.5612 Remote Similarity NPD3574 Clinical (unspecified phase)
0.56 Remote Similarity NPD6080 Approved
0.56 Remote Similarity NPD6904 Approved
0.56 Remote Similarity NPD6051 Approved
0.56 Remote Similarity NPD6673 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