NPASS Compound

Structure

CID147298 OpenBabel06191715522D 34 36 0 0 1 0 0 0 0 0999 V2000 6.9282 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -3.5000 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 1.0000 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 7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7942 -3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 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 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -2.0000 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 7.7942 -4.5000 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 N 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -3.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 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 4.3301 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -1.5000 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 6.9282 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 1 10 2 0 0 0 0 2 4 2 0 0 0 0 2 10 1 0 0 0 0 3 11 2 0 0 0 0 4 11 1 0 0 0 0 5 6 1 0 0 0 0 6 14 1 0 0 0 0 7 22 1 0 0 0 0 8 12 1 0 0 0 0 8 23 1 0 0 0 0 9 27 1 0 0 0 0 9 28 2 0 0 0 0 10 17 1 0 0 0 0 11 22 1 0 0 0 0 12 7 1 1 0 0 0 12 27 1 0 0 0 0 13 5 1 6 0 0 0 13 19 1 0 0 0 0 13 24 1 0 0 0 0 14 29 2 0 0 0 0 14 30 1 0 0 0 0 15 16 2 0 0 0 0 15 18 1 0 0 0 0 15 27 1 0 0 0 0 16 23 1 0 0 0 0 16 25 1 0 0 0 0 17 24 1 0 0 0 0 17 31 2 0 0 0 0 18 26 2 0 0 0 0 18 32 1 0 0 0 0 19 33 2 0 0 0 0 19 34 1 0 0 0 0 20 21 2 0 0 0 0 20 25 1 0 0 0 0 20 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	473.17
Volume:	440.951
LogP:	-2.183
LogD:	-0.581
LogS:	-5.086
# Rotatable Bonds:	11
TPSA:	220.57
# H-Bond Aceptor:	14
# H-Bond Donor:	8
# Rings:	3
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.2
Synthetic Accessibility Score:	3.884
Fsp3:	0.3
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.91
MDCK Permeability:	3.5163378925062716e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.987
Human Intestinal Absorption (HIA):	0.304
20% Bioavailability (F20%):	0.155
30% Bioavailability (F30%):	0.248

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.181
Plasma Protein Binding (PPB):	41.21799087524414%
Volume Distribution (VD):	0.193
Pgp-substrate:	52.37141418457031%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.035
CYP2C19-inhibitor:	0.065
CYP2C19-substrate:	0.028
CYP2C9-inhibitor:	0.209
CYP2C9-substrate:	0.012
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.063
CYP3A4-inhibitor:	0.015
CYP3A4-substrate:	0.005

ADMET: Excretion

Clearance (CL):	3.376
Half-life (T1/2):	0.949

ADMET: Toxicity

hERG Blockers:	0.024
Human Hepatotoxicity (H-HT):	0.967
Drug-inuced Liver Injury (DILI):	0.972
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.02
Maximum Recommended Daily Dose:	0.059
Skin Sensitization:	0.128
Carcinogencity:	0.116
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.092

Download Data

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

Natural Product: NPC147298

Natural Product ID:	NPC147298
*Common Name:**	Folinic Acid
IUPAC Name:	(2S)-2-[[4-[[(6R)-2-amino-5-formyl-4-oxo-1,6,7,8-tetrahydropteridin-6-yl]methylamino]benzoyl]amino]pentanedioic acid
Synonyms:
Standard InCHIKey:	VVIAGPKUTFNRDU-OLZOCXBDSA-N
Standard InCHI:	InChI=1S/C20H23N7O7/c21-20-25-16-15(18(32)26-20)27(9-28)12(8-23-16)7-22-11-3-1-10(2-4-11)17(31)24-13(19(33)34)5-6-14(29)30/h1-4,9,12-13,22H,5-8H2,(H,24,31)(H,29,30)(H,33,34)(H4,21,23,25,26,32)/t12-,13+/m1/s1
SMILES:	c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@@H]1CNc2c(c(nc(=N)[nH]2)O)N1C=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1232801
PubChem CID:	135548
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids and derivatives [CHEMONTID:0004323] Glutamic acid 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27400088]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25538068]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[17997069]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	roots	purchased from Kiu Shun Trading Ltd., Vancouver, Canada	2000	PMID[16643021]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679317]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[11374978]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2921	Angelica acutiloba	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2921	Angelica acutiloba	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

Showing 1 to 10 of 21 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
Others	1
Potency	3

Activity Type	# Activity
NON-MOLECULAR	3
ORGANISM	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Hit score	=	0.1373	n.a.	PMID[499312]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Potency	n.a.	94.3	nM	PMID[499311]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Potency	n.a.	2658.6	nM	PMID[499311]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Potency	n.a.	188.2	nM	PMID[499311]

Showing 1 to 4 of 4 entries

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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 NPC147298 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	461
0.1-0.2	5731
0.2-0.3	13808
0.3-0.4	15981
0.4-0.5	3631
0.5-0.6	2757
0.6-0.7	312
0.7-0.8	6
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	7

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC131450
1.0	High Similarity	NPC182057
0.9812	High Similarity	NPC14849
0.9811	High Similarity	NPC328611
0.9565	High Similarity	NPC248862

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 NPC147298 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	221
0.1-0.2	622
0.2-0.3	995
0.3-0.4	1954
0.4-0.5	2734
0.5-0.6	2164
0.6-0.7	413
0.7-0.8	25
0.8-0.85	5
0.85-0.9	3
0.9-0.95	1
0.95-1	13

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD3999	Approved
1.0	High Similarity	NPD3997	Approved
1.0	High Similarity	NPD3998	Approved
0.9937	High Similarity	NPD3996	Approved
0.9937	High Similarity	NPD3992	Approved

Showing 1 to 5 of 200 entries

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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