NPASS Compound

Structure

CID62272 OpenBabel06191715402D 29 32 0 0 0 0 0 0 0 0999 V2000 -5.0387 -1.9394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5193 -2.4242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1989 -2.4242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6796 -2.9091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0387 -0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5193 -1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3591 -1.9394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8398 -2.4242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1989 0.4848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6796 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8398 -1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1989 -0.4848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6796 -0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3591 -0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8398 -1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5193 -0.4848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3591 0.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8398 0.4848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5193 0.4848 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 -3.3591 1.9394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8398 1.4545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6796 0.9697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8398 0.4848 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1989 2.4242 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5193 2.4242 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6796 1.9394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.9394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 0 0 0 0 1 5 1 0 0 0 0 2 4 2 0 0 0 0 2 6 1 0 0 0 0 3 7 1 0 0 0 0 4 8 1 0 0 0 0 5 12 2 0 0 0 0 6 13 2 0 0 0 0 7 14 2 0 0 0 0 8 15 2 0 0 0 0 9 12 1 0 0 0 0 9 18 2 0 0 0 0 10 13 1 0 0 0 0 10 19 2 0 0 0 0 11 16 1 0 0 0 0 11 17 1 0 0 0 0 12 14 1 0 0 0 0 13 15 1 0 0 0 0 14 16 1 0 0 0 0 15 17 1 0 0 0 0 16 20 2 0 0 0 0 17 21 2 0 0 0 0 18 20 1 0 0 0 0 18 22 1 0 0 0 0 19 21 1 0 0 0 0 19 23 1 0 0 0 0 20 24 1 0 0 0 0 21 25 1 0 0 0 0 22 26 2 0 0 0 0 22 27 1 0 0 0 0 23 28 2 0 0 0 0 23 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	388.09
Volume:	393.242
LogP:	5.94
LogD:	2.43
LogS:	-3.012
# Rotatable Bonds:	4
TPSA:	115.06
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.412
Synthetic Accessibility Score:	2.33
Fsp3:	0.043
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.101
MDCK Permeability:	7.257131073856726e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.996
20% Bioavailability (F20%):	0.11
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.029
Plasma Protein Binding (PPB):	100.02035522460938%
Volume Distribution (VD):	0.282
Pgp-substrate:	0.8700380325317383%

ADMET: Metabolism

CYP1A2-inhibitor:	0.092
CYP1A2-substrate:	0.054
CYP2C19-inhibitor:	0.029
CYP2C19-substrate:	0.041
CYP2C9-inhibitor:	0.462
CYP2C9-substrate:	0.035
CYP2D6-inhibitor:	0.189
CYP2D6-substrate:	0.039
CYP3A4-inhibitor:	0.009
CYP3A4-substrate:	0.016

ADMET: Excretion

Clearance (CL):	0.669
Half-life (T1/2):	0.878

ADMET: Toxicity

hERG Blockers:	0.042
Human Hepatotoxicity (H-HT):	0.742
Drug-inuced Liver Injury (DILI):	0.987
AMES Toxicity:	0.013
Rat Oral Acute Toxicity:	0.31
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.838
Carcinogencity:	0.143
Eye Corrosion:	0.003
Eye Irritation:	0.026
Respiratory Toxicity:	0.859

Download Data

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

Natural Product: NPC62272

Natural Product ID:	NPC62272
*Common Name:**	Pamoic Acid
IUPAC Name:	4-[(3-carboxy-2-hydroxynaphthalen-1-yl)methyl]-3-hydroxynaphthalene-2-carboxylic acid
Synonyms:	Pamoic Acid
Standard InCHIKey:	WLJNZVDCPSBLRP-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C23H16O6/c24-20-16(14-7-3-1-5-12(14)9-18(20)22(26)27)11-17-15-8-4-2-6-13(15)10-19(21(17)25)23(28)29/h1-10,24-25H,11H2,(H,26,27)(H,28,29)
SMILES:	OC(=O)c1cc2ccccc2c(c1O)Cc1c(O)c(cc2c1cccc2)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL177880
PubChem CID:	8546 54742459
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000023] Naphthalenes [CHEMONTID:0001871] Naphthalenecarboxylic acids and derivatives [CHEMONTID:0002421] Naphthalenecarboxylic 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO1470	Fructus psoraleae corylifoliae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]

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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
EC50	5
GI50	55
IC50	5
Ki	1
Others	9
Potency	16

Activity Type	# Activity
Cell Line	56
Individual Protein	15
ORGANISM	6
Others	12
SINGLE PROTEIN	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	""	Potency	n.a.	3349.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	""	Potency	n.a.	16930.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	""	Potency	n.a.	23710.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	""	Potency	n.a.	33491.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	""	Potency	n.a.	37578	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	""	Potency	n.a.	13333.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	""	Potency	n.a.	26603.2	nM	PubChem BioAssay data set
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-0.44	%	PMID[448791]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	0.17	%	PMID[448790]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	14.89	%	PMID[448789]

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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 NPC62272 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	394
0.1-0.2	1754
0.2-0.3	3859
0.3-0.4	10396
0.4-0.5	8638
0.5-0.6	5571
0.6-0.7	8517
0.7-0.8	3286
0.8-0.85	212
0.85-0.9	65
0.9-0.95	4
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9098	High Similarity	NPC474517
0.9098	High Similarity	NPC72669
0.9058	High Similarity	NPC225243
0.9	High Similarity	NPC296752
0.9	High Similarity	NPC236189

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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 NPC62272 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	372
0.1-0.2	959
0.2-0.3	1429
0.3-0.4	2810
0.4-0.5	2057
0.5-0.6	1074
0.6-0.7	356
0.7-0.8	84
0.8-0.85	5
0.85-0.9	3
0.9-0.95	0
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD5404	Approved
1.0	High Similarity	NPD5405	Approved
1.0	High Similarity	NPD5408	Approved
1.0	High Similarity	NPD5406	Approved
0.8803	High Similarity	NPD7390	Discontinued

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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