NPASS Compound

Structure

CID55121 OpenBabel06191715392D 40 43 0 0 1 0 0 0 0 0999 V2000 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 3 5 1 0 0 0 0 4 6 2 0 0 0 0 5 19 2 0 0 0 0 6 19 1 0 0 0 0 7 16 1 0 0 0 0 7 19 1 0 0 0 0 8 12 1 0 0 0 0 8 20 2 0 0 0 0 9 13 2 0 0 0 0 9 20 1 0 0 0 0 10 14 1 0 0 0 0 10 21 2 0 0 0 0 11 15 2 0 0 0 0 11 21 1 0 0 0 0 12 22 2 0 0 0 0 13 22 1 0 0 0 0 14 23 2 0 0 0 0 15 23 1 0 0 0 0 16 24 1 0 0 0 0 17 18 1 0 0 0 0 17 25 1 0 0 0 0 18 1 1 1 0 0 0 18 32 1 0 0 0 0 20 26 1 0 0 0 0 21 27 1 0 0 0 0 22 33 1 0 0 0 0 23 34 1 0 0 0 0 24 35 2 0 0 0 0 24 39 1 0 0 0 0 25 36 2 0 0 0 0 25 40 1 0 0 0 0 26 29 2 0 0 0 0 26 30 1 0 0 0 0 27 28 1 0 0 0 0 27 31 2 0 0 0 0 28 30 2 0 0 0 0 28 37 1 0 0 0 0 29 31 1 0 0 0 0 29 38 1 0 0 0 0 30 39 1 0 0 0 0 31 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	544.17
Volume:	552.708
LogP:	4.518
LogD:	2.72
LogS:	-3.877
# Rotatable Bonds:	11
TPSA:	153.75
# H-Bond Aceptor:	9
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.111
Synthetic Accessibility Score:	3.222
Fsp3:	0.161
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.604
MDCK Permeability:	1.4000296687299851e-05
Pgp-inhibitor:	0.028
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.177
30% Bioavailability (F30%):	0.1

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	100.81553649902344%
Volume Distribution (VD):	0.418
Pgp-substrate:	0.5791574120521545%

ADMET: Metabolism

CYP1A2-inhibitor:	0.909
CYP1A2-substrate:	0.03
CYP2C19-inhibitor:	0.97
CYP2C19-substrate:	0.049
CYP2C9-inhibitor:	0.902
CYP2C9-substrate:	0.973
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.392
CYP3A4-inhibitor:	0.273
CYP3A4-substrate:	0.225

ADMET: Excretion

Clearance (CL):	3.575
Half-life (T1/2):	0.877

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.017
Drug-inuced Liver Injury (DILI):	0.925
AMES Toxicity:	0.058
Rat Oral Acute Toxicity:	0.448
Maximum Recommended Daily Dose:	0.135
Skin Sensitization:	0.503
Carcinogencity:	0.408
Eye Corrosion:	0.003
Eye Irritation:	0.435
Respiratory Toxicity:	0.047

Download Data

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

Natural Product: NPC55121

Natural Product ID:	NPC55121
*Common Name:**	Curtisian K
IUPAC Name:	[2,5-dihydroxy-3,6-bis(4-hydroxyphenyl)-4-(3-phenylpropanoyloxy)phenyl] (3R)-3-hydroxybutanoate
Synonyms:	Curtisian K
Standard InCHIKey:	DBQCFXJEISVQMJ-GOSISDBHSA-N
Standard InCHI:	InChI=1S/C31H28O9/c1-18(32)17-25(36)40-31-27(21-10-14-23(34)15-11-21)28(37)30(26(29(31)38)20-8-12-22(33)13-9-20)39-24(35)16-7-19-5-3-2-4-6-19/h2-6,8-15,18,32-34,37-38H,7,16-17H2,1H3/t18-/m1/s1
SMILES:	C[C@H](CC(=O)Oc1c(c2ccc(cc2)O)c(O)c(c(c1O)c1ccc(cc1)O)OC(=O)CCc1ccccc1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL559794
PubChem CID:	45269176
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0002042] Terphenyls [CHEMONTID:0002126] P-terphenyls

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO16348	Paxillus curtisii	Species	Paxillaceae	Eukaryota	fruiting bodies	Odae National Parks, Korea	n.a.	PMID[19450986]
NPO16348	Paxillus curtisii	Species	Paxillaceae	Eukaryota	n.a.	fruit body	n.a.	PMID[10805570]
NPO16348	Paxillus curtisii	Species	Paxillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16348	Paxillus curtisii	Species	Paxillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

Showing 1 to 4 of 4 entries

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

Activity Type	# Activity
IC50	3

Activity Type	# Activity
NON-MOLECULAR	2
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1	Others	Radical scavenging activity	""	IC50	>	500000.0	nM	PMID[534104]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	11300.0	nM	PMID[534104]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	500000.0	nM	PMID[534104]

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☑ 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 NPC55121 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	372
0.1-0.2	1632
0.2-0.3	3783
0.3-0.4	9621
0.4-0.5	9033
0.5-0.6	3794
0.6-0.7	5424
0.7-0.8	7414
0.8-0.85	1498
0.85-0.9	100
0.9-0.95	17
0.95-1	9

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Similarity Score	Similarity Level	Natural Product ID
0.987	High Similarity	NPC174311
0.9742	High Similarity	NPC476200
0.9742	High Similarity	NPC192258
0.9608	High Similarity	NPC155015
0.9608	High Similarity	NPC292385

Showing 1 to 5 of 200 entries

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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 NPC55121 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	337
0.1-0.2	905
0.2-0.3	1891
0.3-0.4	2634
0.4-0.5	1741
0.5-0.6	981
0.6-0.7	512
0.7-0.8	131
0.8-0.85	13
0.85-0.9	5
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8735	High Similarity	NPD5844	Phase 1
0.8466	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.8443	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.8443	Intermediate Similarity	NPD6166	Phase 2
0.8443	Intermediate Similarity	NPD6167	Clinical (unspecified phase)

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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