Structure

Physi-Chem Properties

Molecular Weight:  432.18
Volume:  438.481
LogP:  2.741
LogD:  -1.768
LogS:  -1.134
# Rotatable Bonds:  6
TPSA:  136.56
# H-Bond Aceptor:  8
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.573
Synthetic Accessibility Score:  4.575
Fsp3:  0.652
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:  -5.481
MDCK Permeability:  2.1185458535910584e-05
Pgp-inhibitor:  0.587
Pgp-substrate:  0.811
Human Intestinal Absorption (HIA):  0.033
20% Bioavailability (F20%):  0.068
30% Bioavailability (F30%):  0.021

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  72.19808197021484%
Volume Distribution (VD):  0.926
Pgp-substrate:  25.196002960205078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.72
CYP2C19-inhibitor:  0.011
CYP2C19-substrate:  0.859
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.177
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.048
CYP3A4-inhibitor:  0.463
CYP3A4-substrate:  0.904

ADMET: Excretion

Clearance (CL):  3.672
Half-life (T1/2):  0.265

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.125
Drug-inuced Liver Injury (DILI):  0.966
AMES Toxicity:  0.022
Rat Oral Acute Toxicity:  1.0
Maximum Recommended Daily Dose:  0.276
Skin Sensitization:  0.029
Carcinogencity:  0.207
Eye Corrosion:  0.996
Eye Irritation:  0.395
Respiratory Toxicity:  0.695

Download Data

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

  Natural Product: NPC138056

Natural Product ID:  NPC138056
Common Name*:   AVXBWZLPMWIFHX-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:   Albaspidin P-P; Albaspidin-Pp
Standard InCHIKey:  AVXBWZLPMWIFHX-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C23H28O8/c1-7-12(24)14-16(26)10(18(28)22(3,4)20(14)30)9-11-17(27)15(13(25)8-2)21(31)23(5,6)19(11)29/h28-31H,7-9H2,1-6H3
SMILES:  CCC(=O)C1=C(C(C)(C)C(=C(CC2=C(C(C)(C)C(=C(C(=O)CC)C2=O)O)O)C1=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL484218
PubChem CID:   NA
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]
NPO28558 Hypericum drummondii Species Hypericaceae Eukaryota n.a. root n.a. PMID[1800634]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. PMID[24013342]
NPO28558 Hypericum drummondii Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[2746258]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28558 Hypericum drummondii Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28558 Hypericum drummondii Species Hypericaceae 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]
NPO28558 Hypericum drummondii Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
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
NPT168 Cell Line P388 Mus musculus ED50 > 50.0 ug ml-1 PMID[560094]
NPT91 Cell Line KB Homo sapiens ED50 > 50.0 ug ml-1 PMID[560094]
NPT865 Individual Protein Fatty acid synthase Homo sapiens IC50 = 60200.0 nM PMID[560093]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 50.0 ug.mL-1 PMID[560094]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 12.5 ug.mL-1 PMID[560094]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 50.0 ug.mL-1 PMID[560094]
NPT19 Organism Escherichia coli Escherichia coli MIC > 100.0 ug.mL-1 PMID[560094]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 100.0 ug.mL-1 PMID[560094]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. ED50 > 50.0 ug ml-1 PMID[560094]

☑ 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 NPC138056 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 NPC15130
1.0 High Similarity NPC473212
1.0 High Similarity NPC254449
1.0 High Similarity NPC115752
0.9828 High Similarity NPC473211
0.9828 High Similarity NPC473210
0.9194 High Similarity NPC473213
0.7424 Intermediate Similarity NPC53109
0.7424 Intermediate Similarity NPC143168
0.7313 Intermediate Similarity NPC7029
0.726 Intermediate Similarity NPC175079
0.7164 Intermediate Similarity NPC477830
0.7164 Intermediate Similarity NPC477707
0.7123 Intermediate Similarity NPC264178
0.7 Intermediate Similarity NPC243272
0.6974 Remote Similarity NPC30321
0.6901 Remote Similarity NPC146376
0.6901 Remote Similarity NPC125578
0.6901 Remote Similarity NPC263382
0.6818 Remote Similarity NPC320421
0.6806 Remote Similarity NPC94488
0.6806 Remote Similarity NPC262673
0.6774 Remote Similarity NPC477458
0.6712 Remote Similarity NPC94743
0.6712 Remote Similarity NPC291062
0.6711 Remote Similarity NPC1254
0.6711 Remote Similarity NPC110725
0.6711 Remote Similarity NPC92080
0.6709 Remote Similarity NPC99308
0.6709 Remote Similarity NPC189237
0.6667 Remote Similarity NPC477452
0.6622 Remote Similarity NPC223187
0.6585 Remote Similarity NPC90287
0.6582 Remote Similarity NPC279667
0.6575 Remote Similarity NPC474060
0.65 Remote Similarity NPC55869
0.65 Remote Similarity NPC475863
0.65 Remote Similarity NPC470034
0.6494 Remote Similarity NPC477708
0.6479 Remote Similarity NPC61473
0.6479 Remote Similarity NPC251118
0.6456 Remote Similarity NPC27817
0.6429 Remote Similarity NPC32285
0.6429 Remote Similarity NPC288253
0.642 Remote Similarity NPC477270
0.642 Remote Similarity NPC477271
0.642 Remote Similarity NPC477269
0.642 Remote Similarity NPC129080
0.6418 Remote Similarity NPC192843
0.6406 Remote Similarity NPC137396
0.64 Remote Similarity NPC84790
0.64 Remote Similarity NPC144627
0.6386 Remote Similarity NPC311702
0.6386 Remote Similarity NPC472931
0.6386 Remote Similarity NPC94531
0.6386 Remote Similarity NPC472940
0.6386 Remote Similarity NPC123319
0.6375 Remote Similarity NPC108955
0.6375 Remote Similarity NPC287063
0.6375 Remote Similarity NPC26139
0.6349 Remote Similarity NPC116906
0.6341 Remote Similarity NPC258985
0.6338 Remote Similarity NPC474400
0.6338 Remote Similarity NPC150162
0.6338 Remote Similarity NPC34622
0.6338 Remote Similarity NPC4638
0.6333 Remote Similarity NPC25771
0.6329 Remote Similarity NPC74410
0.6329 Remote Similarity NPC189485
0.6324 Remote Similarity NPC56905
0.6324 Remote Similarity NPC27610
0.6301 Remote Similarity NPC474619
0.6296 Remote Similarity NPC472684
0.6296 Remote Similarity NPC44963
0.6296 Remote Similarity NPC225515
0.6286 Remote Similarity NPC97322
0.6282 Remote Similarity NPC26504
0.6282 Remote Similarity NPC470525
0.6282 Remote Similarity NPC180886
0.6267 Remote Similarity NPC173321
0.6265 Remote Similarity NPC209882
0.625 Remote Similarity NPC192329
0.625 Remote Similarity NPC98897
0.6234 Remote Similarity NPC147438
0.623 Remote Similarity NPC191337
0.622 Remote Similarity NPC103486
0.6216 Remote Similarity NPC260474
0.6216 Remote Similarity NPC188292
0.6216 Remote Similarity NPC134385
0.6216 Remote Similarity NPC87141
0.6197 Remote Similarity NPC57463
0.6197 Remote Similarity NPC151728
0.619 Remote Similarity NPC8518
0.619 Remote Similarity NPC11711
0.619 Remote Similarity NPC263997
0.619 Remote Similarity NPC473038
0.619 Remote Similarity NPC32037
0.619 Remote Similarity NPC132228
0.619 Remote Similarity NPC8571
0.619 Remote Similarity NPC145311
0.618 Remote Similarity NPC14322
0.6176 Remote Similarity NPC283502
0.6176 Remote Similarity NPC281230
0.6176 Remote Similarity NPC193695
0.6176 Remote Similarity NPC192427
0.6173 Remote Similarity NPC74086
0.6167 Remote Similarity NPC292463
0.6164 Remote Similarity NPC16119
0.6154 Remote Similarity NPC469803
0.6145 Remote Similarity NPC470015
0.6145 Remote Similarity NPC41539
0.6145 Remote Similarity NPC105803
0.6145 Remote Similarity NPC168188
0.6143 Remote Similarity NPC127582
0.6133 Remote Similarity NPC469914
0.6133 Remote Similarity NPC256846
0.6129 Remote Similarity NPC4079
0.6129 Remote Similarity NPC14917
0.6129 Remote Similarity NPC236355
0.6125 Remote Similarity NPC476808
0.6118 Remote Similarity NPC229717
0.6118 Remote Similarity NPC203795
0.6111 Remote Similarity NPC473902
0.6104 Remote Similarity NPC56747
0.6104 Remote Similarity NPC247586
0.6104 Remote Similarity NPC180015
0.6104 Remote Similarity NPC109576
0.6104 Remote Similarity NPC130016
0.6098 Remote Similarity NPC116797
0.6094 Remote Similarity NPC474391
0.6094 Remote Similarity NPC228776
0.6094 Remote Similarity NPC15325
0.6094 Remote Similarity NPC32351
0.6081 Remote Similarity NPC475523
0.6066 Remote Similarity NPC477686
0.6061 Remote Similarity NPC474141
0.6056 Remote Similarity NPC40082
0.6056 Remote Similarity NPC475795
0.6053 Remote Similarity NPC246722
0.6053 Remote Similarity NPC151045
0.6049 Remote Similarity NPC19900
0.6049 Remote Similarity NPC475681
0.6047 Remote Similarity NPC272039
0.6047 Remote Similarity NPC99909
0.6047 Remote Similarity NPC220930
0.6029 Remote Similarity NPC473733
0.6027 Remote Similarity NPC296436
0.6027 Remote Similarity NPC176215
0.6027 Remote Similarity NPC470329
0.6026 Remote Similarity NPC470299
0.6024 Remote Similarity NPC302661
0.6024 Remote Similarity NPC238991
0.6024 Remote Similarity NPC469325
0.6 Remote Similarity NPC165711
0.6 Remote Similarity NPC473536
0.6 Remote Similarity NPC259261
0.6 Remote Similarity NPC276764
0.6 Remote Similarity NPC241512
0.6 Remote Similarity NPC155198
0.6 Remote Similarity NPC6185
0.6 Remote Similarity NPC274927
0.6 Remote Similarity NPC33881
0.6 Remote Similarity NPC307112
0.6 Remote Similarity NPC474680
0.6 Remote Similarity NPC472304
0.6 Remote Similarity NPC106851
0.6 Remote Similarity NPC255174
0.6 Remote Similarity NPC64866
0.6 Remote Similarity NPC310992
0.6 Remote Similarity NPC266124
0.5977 Remote Similarity NPC475001
0.5977 Remote Similarity NPC185059
0.5977 Remote Similarity NPC143025
0.5977 Remote Similarity NPC53454
0.5977 Remote Similarity NPC307298
0.5977 Remote Similarity NPC476796
0.5976 Remote Similarity NPC18955
0.5976 Remote Similarity NPC47653
0.5976 Remote Similarity NPC2482
0.5974 Remote Similarity NPC5701
0.5974 Remote Similarity NPC474562
0.5974 Remote Similarity NPC181204
0.5974 Remote Similarity NPC133253
0.597 Remote Similarity NPC87394
0.597 Remote Similarity NPC250539
0.5952 Remote Similarity NPC62214
0.5952 Remote Similarity NPC53733
0.5952 Remote Similarity NPC102197
0.5952 Remote Similarity NPC185256
0.5952 Remote Similarity NPC49019
0.5949 Remote Similarity NPC476346
0.5942 Remote Similarity NPC115385
0.5926 Remote Similarity NPC478247
0.5926 Remote Similarity NPC478246
0.5926 Remote Similarity NPC178852
0.5926 Remote Similarity NPC275494
0.5926 Remote Similarity NPC475994
0.5926 Remote Similarity NPC471409
0.5921 Remote Similarity NPC139397
0.5921 Remote Similarity NPC67608

  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 NPC138056 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
0.7424 Intermediate Similarity NPD2664 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD4627 Clinical (unspecified phase)
0.7101 Intermediate Similarity NPD3704 Approved
0.6479 Remote Similarity NPD7341 Phase 2
0.6389 Remote Similarity NPD7331 Phase 2
0.6375 Remote Similarity NPD4695 Discontinued
0.6203 Remote Similarity NPD4756 Discovery
0.6173 Remote Similarity NPD8259 Clinical (unspecified phase)
0.6164 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6125 Remote Similarity NPD3617 Approved
0.5974 Remote Similarity NPD5276 Approved
0.5921 Remote Similarity NPD4137 Phase 3
0.5909 Remote Similarity NPD7285 Clinical (unspecified phase)
0.5844 Remote Similarity NPD4691 Approved
0.5844 Remote Similarity NPD4747 Approved
0.5823 Remote Similarity NPD5733 Approved
0.5823 Remote Similarity NPD4687 Approved
0.5714 Remote Similarity NPD8779 Phase 3
0.5647 Remote Similarity NPD4221 Approved
0.5647 Remote Similarity NPD4223 Phase 3
0.5625 Remote Similarity NPD4058 Approved
0.5618 Remote Similarity NPD4518 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