Structure

Physi-Chem Properties

Molecular Weight:  150.07
Volume:  156.778
LogP:  1.537
LogD:  1.539
LogS:  -1.862
# Rotatable Bonds:  0
TPSA:  30.21
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.561
Synthetic Accessibility Score:  2.367
Fsp3:  0.444
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:  -4.663
MDCK Permeability:  2.6860869184019975e-05
Pgp-inhibitor:  0.03
Pgp-substrate:  0.152
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.93
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.247
Plasma Protein Binding (PPB):  90.23812103271484%
Volume Distribution (VD):  1.978
Pgp-substrate:  17.327512741088867%

ADMET: Metabolism

CYP1A2-inhibitor:  0.952
CYP1A2-substrate:  0.903
CYP2C19-inhibitor:  0.548
CYP2C19-substrate:  0.092
CYP2C9-inhibitor:  0.145
CYP2C9-substrate:  0.821
CYP2D6-inhibitor:  0.595
CYP2D6-substrate:  0.859
CYP3A4-inhibitor:  0.05
CYP3A4-substrate:  0.225

ADMET: Excretion

Clearance (CL):  9.247
Half-life (T1/2):  0.675

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.798
Drug-inuced Liver Injury (DILI):  0.785
AMES Toxicity:  0.214
Rat Oral Acute Toxicity:  0.151
Maximum Recommended Daily Dose:  0.094
Skin Sensitization:  0.292
Carcinogencity:  0.776
Eye Corrosion:  0.111
Eye Irritation:  0.644
Respiratory Toxicity:  0.187

Download Data

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

  Natural Product: NPC429928

Natural Product ID:  NPC429928
Common Name*:   5,7-Dihydrocoumarin
IUPAC Name:   5,6,7,8-tetrahydrochromen-2-one
Synonyms:   5,7-Dihydrocoumarin
Standard InCHIKey:  TUCYOPUMAOACER-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H10O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h5-6H,1-4H2
SMILES:  C1CCc2c(C1)ccc(=O)o2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL465435
PubChem CID:   3964390
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
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota n.a. root n.a. PMID[11395279]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota whole plants n.a. n.a. PMID[11678652]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota whole plants Shawnee National Forest, Harrisburg, IL, US n.a. PMID[11678652]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota n.a. n.a. n.a. PMID[12419367]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota leaves Kaohsiung, Taiwan 2006-SEP PMID[18986201]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota Fruits n.a. n.a. PMID[19296617]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota n.a. formosan n.a. PMID[8864236]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota n.a. n.a. n.a. PMID[9358644]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5495 Broussonetia papyrifera Species Moraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5495 Broussonetia papyrifera Species Moraceae 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
NPT441 Individual Protein Cytochrome P450 19A1 Homo sapiens IC50 > 40.0 ug.mL-1 PMID[541981]

☑ 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 NPC429928 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
0.8621 High Similarity NPC86948
0.7903 Intermediate Similarity NPC133600
0.7761 Intermediate Similarity NPC313444
0.7656 Intermediate Similarity NPC15193
0.7627 Intermediate Similarity NPC191643
0.7576 Intermediate Similarity NPC471556
0.7541 Intermediate Similarity NPC173157
0.7536 Intermediate Similarity NPC315285
0.7536 Intermediate Similarity NPC315597
0.7536 Intermediate Similarity NPC316029
0.7463 Intermediate Similarity NPC315115
0.7419 Intermediate Similarity NPC150717
0.7414 Intermediate Similarity NPC234084
0.7353 Intermediate Similarity NPC132286
0.7344 Intermediate Similarity NPC22897
0.7344 Intermediate Similarity NPC159650
0.7313 Intermediate Similarity NPC471566
0.7313 Intermediate Similarity NPC182794
0.7313 Intermediate Similarity NPC471565
0.7258 Intermediate Similarity NPC25038
0.7246 Intermediate Similarity NPC238223
0.7206 Intermediate Similarity NPC469446
0.7206 Intermediate Similarity NPC191233
0.7183 Intermediate Similarity NPC133098
0.7164 Intermediate Similarity NPC477457
0.7164 Intermediate Similarity NPC477456
0.7162 Intermediate Similarity NPC54996
0.7143 Intermediate Similarity NPC232812
0.7143 Intermediate Similarity NPC470693
0.7143 Intermediate Similarity NPC221763
0.7121 Intermediate Similarity NPC68044
0.7097 Intermediate Similarity NPC218486
0.7059 Intermediate Similarity NPC220766
0.7042 Intermediate Similarity NPC37929
0.7042 Intermediate Similarity NPC64234
0.7 Intermediate Similarity NPC477117
0.6984 Remote Similarity NPC478117
0.697 Remote Similarity NPC309408
0.6957 Remote Similarity NPC37382
0.6944 Remote Similarity NPC181587
0.6933 Remote Similarity NPC316324
0.6933 Remote Similarity NPC473825
0.6933 Remote Similarity NPC315394
0.6901 Remote Similarity NPC475004
0.6825 Remote Similarity NPC478120
0.6765 Remote Similarity NPC210303
0.6765 Remote Similarity NPC179087
0.6765 Remote Similarity NPC2328
0.6765 Remote Similarity NPC44343
0.6761 Remote Similarity NPC474823
0.6761 Remote Similarity NPC475760
0.6761 Remote Similarity NPC218477
0.6716 Remote Similarity NPC26223
0.6716 Remote Similarity NPC79756
0.6714 Remote Similarity NPC470033
0.6707 Remote Similarity NPC125925
0.6667 Remote Similarity NPC265574
0.6667 Remote Similarity NPC53136
0.6667 Remote Similarity NPC151481
0.6667 Remote Similarity NPC329826
0.6667 Remote Similarity NPC189700
0.6667 Remote Similarity NPC473277
0.6667 Remote Similarity NPC469414
0.6667 Remote Similarity NPC173409
0.6625 Remote Similarity NPC288281
0.662 Remote Similarity NPC21998
0.6618 Remote Similarity NPC217537
0.6588 Remote Similarity NPC32944
0.6588 Remote Similarity NPC193396
0.6585 Remote Similarity NPC291712
0.6579 Remote Similarity NPC261732
0.6571 Remote Similarity NPC476589
0.6571 Remote Similarity NPC470688
0.6567 Remote Similarity NPC203233
0.6533 Remote Similarity NPC470686
0.6528 Remote Similarity NPC280374
0.6528 Remote Similarity NPC287705
0.6528 Remote Similarity NPC134385
0.6528 Remote Similarity NPC79220
0.6522 Remote Similarity NPC217940
0.6522 Remote Similarity NPC155849
0.6522 Remote Similarity NPC473737
0.6522 Remote Similarity NPC132243
0.6506 Remote Similarity NPC96625
0.6494 Remote Similarity NPC475711
0.6494 Remote Similarity NPC471225
0.6494 Remote Similarity NPC47069
0.6486 Remote Similarity NPC475762
0.6479 Remote Similarity NPC248125
0.6479 Remote Similarity NPC116013
0.6471 Remote Similarity NPC299730
0.6471 Remote Similarity NPC19241
0.6471 Remote Similarity NPC98519
0.6471 Remote Similarity NPC130953
0.6463 Remote Similarity NPC281172
0.6456 Remote Similarity NPC268827
0.6452 Remote Similarity NPC236338
0.6452 Remote Similarity NPC275316
0.6429 Remote Similarity NPC25747
0.6429 Remote Similarity NPC148233
0.6429 Remote Similarity NPC308457
0.642 Remote Similarity NPC475083
0.641 Remote Similarity NPC315765
0.64 Remote Similarity NPC185186
0.64 Remote Similarity NPC327383
0.64 Remote Similarity NPC329914
0.64 Remote Similarity NPC329890
0.64 Remote Similarity NPC474705
0.6393 Remote Similarity NPC128520
0.6389 Remote Similarity NPC203335
0.6389 Remote Similarity NPC472266
0.6389 Remote Similarity NPC225272
0.6375 Remote Similarity NPC71795
0.6364 Remote Similarity NPC51846
0.6364 Remote Similarity NPC40353
0.6353 Remote Similarity NPC142159
0.6353 Remote Similarity NPC95364
0.6351 Remote Similarity NPC469660
0.6351 Remote Similarity NPC476012
0.6351 Remote Similarity NPC476037
0.6351 Remote Similarity NPC59558
0.6338 Remote Similarity NPC133904
0.6338 Remote Similarity NPC96414
0.6333 Remote Similarity NPC270706
0.6324 Remote Similarity NPC473494
0.6324 Remote Similarity NPC286189
0.6324 Remote Similarity NPC474267
0.6296 Remote Similarity NPC123908
0.6296 Remote Similarity NPC10080
0.629 Remote Similarity NPC126184
0.629 Remote Similarity NPC15912
0.6282 Remote Similarity NPC41780
0.6282 Remote Similarity NPC180290
0.6282 Remote Similarity NPC68156
0.6282 Remote Similarity NPC187568
0.6279 Remote Similarity NPC224270
0.6267 Remote Similarity NPC186531
0.6267 Remote Similarity NPC178575
0.6267 Remote Similarity NPC84038
0.6267 Remote Similarity NPC316185
0.6265 Remote Similarity NPC307112
0.625 Remote Similarity NPC124586
0.625 Remote Similarity NPC146811
0.625 Remote Similarity NPC201356
0.625 Remote Similarity NPC106531
0.6235 Remote Similarity NPC472302
0.6234 Remote Similarity NPC327041
0.6234 Remote Similarity NPC285840
0.6234 Remote Similarity NPC228978
0.623 Remote Similarity NPC128280
0.6207 Remote Similarity NPC166110
0.6207 Remote Similarity NPC32552
0.6203 Remote Similarity NPC475699
0.6197 Remote Similarity NPC226066
0.6197 Remote Similarity NPC114464
0.6197 Remote Similarity NPC475618
0.619 Remote Similarity NPC15789
0.619 Remote Similarity NPC27264
0.6184 Remote Similarity NPC287878
0.6184 Remote Similarity NPC276336
0.6173 Remote Similarity NPC471552
0.6173 Remote Similarity NPC42470
0.6173 Remote Similarity NPC473339
0.6154 Remote Similarity NPC188860
0.6154 Remote Similarity NPC473223
0.6145 Remote Similarity NPC196487
0.6145 Remote Similarity NPC14575
0.6143 Remote Similarity NPC151648
0.6143 Remote Similarity NPC26810
0.6136 Remote Similarity NPC1108
0.6136 Remote Similarity NPC248193
0.6133 Remote Similarity NPC67183
0.6129 Remote Similarity NPC90490
0.6125 Remote Similarity NPC63649
0.6125 Remote Similarity NPC271632
0.6125 Remote Similarity NPC264227
0.6125 Remote Similarity NPC473980
0.6125 Remote Similarity NPC150646
0.6125 Remote Similarity NPC473981
0.6125 Remote Similarity NPC469617
0.6125 Remote Similarity NPC139712
0.6125 Remote Similarity NPC472965
0.6119 Remote Similarity NPC141699
0.6119 Remote Similarity NPC324224
0.6119 Remote Similarity NPC245002
0.6119 Remote Similarity NPC472808
0.6118 Remote Similarity NPC199382
0.6118 Remote Similarity NPC113370
0.6118 Remote Similarity NPC103743
0.6118 Remote Similarity NPC476079
0.6118 Remote Similarity NPC316138
0.6118 Remote Similarity NPC313658
0.6111 Remote Similarity NPC131174
0.6104 Remote Similarity NPC476355
0.6104 Remote Similarity NPC107654
0.6104 Remote Similarity NPC315843
0.6098 Remote Similarity NPC99240
0.6094 Remote Similarity NPC148056
0.6092 Remote Similarity NPC469372
0.6087 Remote Similarity NPC222852

  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 NPC429928 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
0.6494 Remote Similarity NPD4756 Discovery
0.6338 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6234 Remote Similarity NPD8039 Approved
0.6197 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6071 Remote Similarity NPD1694 Approved
0.6032 Remote Similarity NPD4220 Pre-registration
0.6027 Remote Similarity NPD6108 Clinical (unspecified phase)
0.593 Remote Similarity NPD1282 Approved
0.5915 Remote Similarity NPD4193 Approved
0.5915 Remote Similarity NPD4191 Approved
0.5915 Remote Similarity NPD4194 Approved
0.5915 Remote Similarity NPD4192 Approved
0.5904 Remote Similarity NPD5209 Approved
0.5846 Remote Similarity NPD6927 Phase 3
0.5714 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5616 Remote Similarity NPD2664 Clinical (unspecified phase)

  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