Structure

Physi-Chem Properties

Molecular Weight:  432.18
Volume:  438.481
LogP:  3.178
LogD:  0.273
LogS:  -1.934
# Rotatable Bonds:  7
TPSA:  146.04
# H-Bond Aceptor:  8
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.44
Synthetic Accessibility Score:  4.106
Fsp3:  0.522
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  2
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.911
MDCK Permeability:  1.3623921404359862e-05
Pgp-inhibitor:  0.801
Pgp-substrate:  0.99
Human Intestinal Absorption (HIA):  0.038
20% Bioavailability (F20%):  0.548
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.012
Plasma Protein Binding (PPB):  92.68463897705078%
Volume Distribution (VD):  0.657
Pgp-substrate:  3.756542921066284%

ADMET: Metabolism

CYP1A2-inhibitor:  0.025
CYP1A2-substrate:  0.772
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.407
CYP2C9-inhibitor:  0.107
CYP2C9-substrate:  0.923
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.15
CYP3A4-inhibitor:  0.577
CYP3A4-substrate:  0.541

ADMET: Excretion

Clearance (CL):  12.811
Half-life (T1/2):  0.328

ADMET: Toxicity

hERG Blockers:  0.035
Human Hepatotoxicity (H-HT):  0.094
Drug-inuced Liver Injury (DILI):  0.941
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.826
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.159
Carcinogencity:  0.262
Eye Corrosion:  0.005
Eye Irritation:  0.48
Respiratory Toxicity:  0.327

Download Data

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

  Natural Product: NPC473211

Natural Product ID:  NPC473211
Common Name*:   HJYKGLXKSXYGPR-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HJYKGLXKSXYGPR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C23H28O8/c1-6-8-14(25)15-18(27)10(3)17(26)11(19(15)28)9-12-20(29)16(13(24)7-2)22(31)23(4,5)21(12)30/h10,26-27,30-31H,6-9H2,1-5H3
SMILES:  CCCC(=O)C1=C(O)C(C)C(=C(C1=O)CC1=C(O)C(C(=C(C1=O)C(=O)CC)O)(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3706851
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0003889] Vinylogous acids

*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
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. rhizome n.a. PMID[12951487]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. PMID[16870425]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. PMID[24013342]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae 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
NPT865 Individual Protein Fatty acid synthase Homo sapiens IC50 = 23100.0 nM PMID[496454]

☑ 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 NPC473211 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 NPC473210
0.9828 High Similarity NPC473212
0.9828 High Similarity NPC254449
0.9828 High Similarity NPC15130
0.9828 High Similarity NPC138056
0.9828 High Similarity NPC115752
0.9355 High Similarity NPC473213
0.7397 Intermediate Similarity NPC175079
0.7313 Intermediate Similarity NPC143168
0.7313 Intermediate Similarity NPC53109
0.7206 Intermediate Similarity NPC7029
0.7105 Intermediate Similarity NPC30321
0.7059 Intermediate Similarity NPC477707
0.7059 Intermediate Similarity NPC477830
0.7027 Intermediate Similarity NPC264178
0.6901 Remote Similarity NPC243272
0.6842 Remote Similarity NPC92080
0.6842 Remote Similarity NPC110725
0.6842 Remote Similarity NPC1254
0.6835 Remote Similarity NPC99308
0.6835 Remote Similarity NPC189237
0.6806 Remote Similarity NPC146376
0.6806 Remote Similarity NPC263382
0.6806 Remote Similarity NPC125578
0.6757 Remote Similarity NPC223187
0.6716 Remote Similarity NPC320421
0.6712 Remote Similarity NPC474060
0.6712 Remote Similarity NPC262673
0.6712 Remote Similarity NPC94488
0.6709 Remote Similarity NPC279667
0.6707 Remote Similarity NPC90287
0.6667 Remote Similarity NPC477458
0.6625 Remote Similarity NPC55869
0.6625 Remote Similarity NPC475863
0.6625 Remote Similarity NPC470034
0.6622 Remote Similarity NPC291062
0.6622 Remote Similarity NPC94743
0.662 Remote Similarity NPC251118
0.662 Remote Similarity NPC61473
0.6582 Remote Similarity NPC27817
0.6575 Remote Similarity NPC477452
0.6543 Remote Similarity NPC129080
0.6543 Remote Similarity NPC477269
0.6543 Remote Similarity NPC477270
0.6543 Remote Similarity NPC477271
0.6506 Remote Similarity NPC94531
0.6506 Remote Similarity NPC472931
0.6506 Remote Similarity NPC123319
0.6506 Remote Similarity NPC472940
0.6506 Remote Similarity NPC311702
0.65 Remote Similarity NPC108955
0.65 Remote Similarity NPC287063
0.65 Remote Similarity NPC26139
0.6479 Remote Similarity NPC150162
0.6471 Remote Similarity NPC56905
0.6471 Remote Similarity NPC27610
0.6463 Remote Similarity NPC258985
0.6456 Remote Similarity NPC74410
0.6456 Remote Similarity NPC189485
0.6429 Remote Similarity NPC97322
0.642 Remote Similarity NPC472684
0.642 Remote Similarity NPC44963
0.642 Remote Similarity NPC225515
0.641 Remote Similarity NPC26504
0.641 Remote Similarity NPC180886
0.641 Remote Similarity NPC477708
0.641 Remote Similarity NPC470525
0.6386 Remote Similarity NPC209882
0.6375 Remote Similarity NPC192329
0.6364 Remote Similarity NPC147438
0.6351 Remote Similarity NPC87141
0.6351 Remote Similarity NPC188292
0.6351 Remote Similarity NPC260474
0.6341 Remote Similarity NPC103486
0.6338 Remote Similarity NPC32285
0.6338 Remote Similarity NPC288253
0.6324 Remote Similarity NPC193695
0.6324 Remote Similarity NPC192843
0.6324 Remote Similarity NPC192427
0.6316 Remote Similarity NPC84790
0.6316 Remote Similarity NPC144627
0.631 Remote Similarity NPC132228
0.631 Remote Similarity NPC8571
0.631 Remote Similarity NPC11711
0.631 Remote Similarity NPC8518
0.631 Remote Similarity NPC263997
0.631 Remote Similarity NPC473038
0.631 Remote Similarity NPC32037
0.6308 Remote Similarity NPC137396
0.629 Remote Similarity NPC4079
0.629 Remote Similarity NPC236355
0.629 Remote Similarity NPC14917
0.6286 Remote Similarity NPC127582
0.6282 Remote Similarity NPC469803
0.6267 Remote Similarity NPC256846
0.6267 Remote Similarity NPC469914
0.6265 Remote Similarity NPC41539
0.6265 Remote Similarity NPC470015
0.6265 Remote Similarity NPC168188
0.6265 Remote Similarity NPC105803
0.625 Remote Similarity NPC116906
0.625 Remote Similarity NPC476808
0.625 Remote Similarity NPC474400
0.625 Remote Similarity NPC32351
0.625 Remote Similarity NPC34622
0.625 Remote Similarity NPC473902
0.625 Remote Similarity NPC4638
0.6235 Remote Similarity NPC229717
0.6235 Remote Similarity NPC203795
0.6234 Remote Similarity NPC56747
0.6234 Remote Similarity NPC109576
0.6234 Remote Similarity NPC130016
0.6234 Remote Similarity NPC180015
0.623 Remote Similarity NPC25771
0.622 Remote Similarity NPC116797
0.6216 Remote Similarity NPC475523
0.6216 Remote Similarity NPC474619
0.6212 Remote Similarity NPC474141
0.6197 Remote Similarity NPC475795
0.6184 Remote Similarity NPC246722
0.6184 Remote Similarity NPC173321
0.6184 Remote Similarity NPC151045
0.6176 Remote Similarity NPC473733
0.6173 Remote Similarity NPC19900
0.6173 Remote Similarity NPC475681
0.6164 Remote Similarity NPC470329
0.6164 Remote Similarity NPC98897
0.6163 Remote Similarity NPC220930
0.6163 Remote Similarity NPC99909
0.6163 Remote Similarity NPC272039
0.6154 Remote Similarity NPC470299
0.6145 Remote Similarity NPC238991
0.6145 Remote Similarity NPC302661
0.6145 Remote Similarity NPC469325
0.6143 Remote Similarity NPC259261
0.6143 Remote Similarity NPC472304
0.6143 Remote Similarity NPC276764
0.6133 Remote Similarity NPC134385
0.6133 Remote Similarity NPC155198
0.6133 Remote Similarity NPC310992
0.6129 Remote Similarity NPC191337
0.6125 Remote Similarity NPC266124
0.6125 Remote Similarity NPC165711
0.6118 Remote Similarity NPC241512
0.6118 Remote Similarity NPC33881
0.6118 Remote Similarity NPC6185
0.6118 Remote Similarity NPC474680
0.6118 Remote Similarity NPC255174
0.6111 Remote Similarity NPC151728
0.6111 Remote Similarity NPC14322
0.6111 Remote Similarity NPC57463
0.6104 Remote Similarity NPC474562
0.6104 Remote Similarity NPC181204
0.6104 Remote Similarity NPC5701
0.6104 Remote Similarity NPC133253
0.6098 Remote Similarity NPC74086
0.6098 Remote Similarity NPC2482
0.6098 Remote Similarity NPC18955
0.6094 Remote Similarity NPC145311
0.6092 Remote Similarity NPC143025
0.6092 Remote Similarity NPC307298
0.6092 Remote Similarity NPC53454
0.6092 Remote Similarity NPC476796
0.6087 Remote Similarity NPC283502
0.6087 Remote Similarity NPC115385
0.6087 Remote Similarity NPC281230
0.6081 Remote Similarity NPC16119
0.6076 Remote Similarity NPC476346
0.6071 Remote Similarity NPC49019
0.6071 Remote Similarity NPC53733
0.6071 Remote Similarity NPC102197
0.6066 Remote Similarity NPC292463
0.6053 Remote Similarity NPC67608
0.6053 Remote Similarity NPC139397
0.6049 Remote Similarity NPC178852
0.6049 Remote Similarity NPC275494
0.6049 Remote Similarity NPC478246
0.6049 Remote Similarity NPC471409
0.6049 Remote Similarity NPC475994
0.6049 Remote Similarity NPC478247
0.6032 Remote Similarity NPC8610
0.6032 Remote Similarity NPC262558
0.6029 Remote Similarity NPC275472
0.6027 Remote Similarity NPC475124
0.6027 Remote Similarity NPC285371
0.6027 Remote Similarity NPC212210
0.6026 Remote Similarity NPC247586
0.6026 Remote Similarity NPC474488
0.6024 Remote Similarity NPC278459
0.6024 Remote Similarity NPC475833
0.6024 Remote Similarity NPC121984
0.6024 Remote Similarity NPC275766
0.6023 Remote Similarity NPC65615
0.6023 Remote Similarity NPC112454
0.6023 Remote Similarity NPC474918
0.6023 Remote Similarity NPC68148
0.6 Remote Similarity NPC228776
0.6 Remote Similarity NPC263582
0.6 Remote Similarity NPC474391
0.6 Remote Similarity NPC311852

  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 NPC473211 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
0.7313 Intermediate Similarity NPD2664 Clinical (unspecified phase)
0.7031 Intermediate Similarity NPD4627 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD3704 Approved
0.662 Remote Similarity NPD7341 Phase 2
0.65 Remote Similarity NPD4695 Discontinued
0.6301 Remote Similarity NPD7331 Phase 2
0.625 Remote Similarity NPD3617 Approved
0.6125 Remote Similarity NPD4756 Discovery
0.6104 Remote Similarity NPD5276 Approved
0.6098 Remote Similarity NPD8259 Clinical (unspecified phase)
0.6081 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6053 Remote Similarity NPD4137 Phase 3
0.6023 Remote Similarity NPD7285 Clinical (unspecified phase)
0.5974 Remote Similarity NPD4691 Approved
0.5974 Remote Similarity NPD4747 Approved
0.5949 Remote Similarity NPD5733 Approved
0.5949 Remote Similarity NPD4687 Approved
0.5765 Remote Similarity NPD4221 Approved
0.5765 Remote Similarity NPD4223 Phase 3
0.575 Remote Similarity NPD4058 Approved
0.573 Remote Similarity NPD4518 Approved
0.5699 Remote Similarity NPD4629 Approved
0.5699 Remote Similarity NPD5210 Approved
0.5682 Remote Similarity NPD5279 Phase 3
0.5682 Remote Similarity NPD5690 Phase 2
0.5682 Remote Similarity NPD5280 Approved
0.5682 Remote Similarity NPD4694 Approved
0.5682 Remote Similarity NPD3574 Clinical (unspecified phase)
0.5667 Remote Similarity NPD4753 Phase 2
0.5647 Remote Similarity NPD4692 Approved
0.5647 Remote Similarity NPD4139 Approved
0.5638 Remote Similarity NPD7614 Phase 1
0.5634 Remote Similarity NPD8779 Phase 3
0.5632 Remote Similarity NPD3133 Approved
0.5632 Remote Similarity NPD3666 Approved
0.5632 Remote Similarity NPD4197 Approved
0.5632 Remote Similarity NPD3665 Phase 1

  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