NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	238.07
Volume:	213.073
LogP:	-1.962
LogD:	-0.83
LogS:	-1.189
# Rotatable Bonds:	2
TPSA:	99.12
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.687
Synthetic Accessibility Score:	2.319
Fsp3:	0.333
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.838
MDCK Permeability:	3.638046473497525e-05
Pgp-inhibitor:	0.012
Pgp-substrate:	0.863
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.752
Plasma Protein Binding (PPB):	50.56964874267578%
Volume Distribution (VD):	0.866
Pgp-substrate:	50.342620849609375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.016
CYP1A2-substrate:	0.561
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.057
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.883
CYP2D6-inhibitor:	0.01
CYP2D6-substrate:	0.114
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.169

ADMET: Excretion

Clearance (CL):	1.315
Half-life (T1/2):	0.747

ADMET: Toxicity

hERG Blockers:	0.022
Human Hepatotoxicity (H-HT):	0.245
Drug-inuced Liver Injury (DILI):	0.924
AMES Toxicity:	0.04
Rat Oral Acute Toxicity:	0.042
Maximum Recommended Daily Dose:	0.012
Skin Sensitization:	0.047
Carcinogencity:	0.04
Eye Corrosion:	0.003
Eye Irritation:	0.112
Respiratory Toxicity:	0.264

Download Data

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

Natural Product: NPC180493

Natural Product ID:	NPC180493
*Common Name:**	Acefylline
IUPAC Name:	2-(1,3-dimethyl-2,6-dioxopurin-7-yl)acetic acid
Synonyms:
Standard InCHIKey:	HCYFGRCYSCXKNQ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C9H10N4O4/c1-11-7-6(8(16)12(2)9(11)17)13(4-10-7)3-5(14)15/h4H,3H2,1-2H3,(H,14,15)
SMILES:	OC(=O)Cn1cnc2c1c(=O)n(C)c(=O)n2C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL70246
PubChem CID:	69550
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001797] Imidazopyrimidines [CHEMONTID:0000245] Purines and purine derivatives [CHEMONTID:0000247] Xanthines

*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
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[12575075]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	stem	n.a.	PMID[12575075]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[15577255]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30188125]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29463	Pogostemon cablin	Species	Lamiaceae	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

Activity Type	# Activity
AC50	2
IC50	2
Ki	1
Others	9
Potency	1

Activity Type	# Activity
Individual Protein	1
ORGANISM	7
Others	6
SINGLE PROTEIN	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT4059	Individual Protein	Adenosine A2b receptor	Homo sapiens	Ki	=	27600.0	nM	PMID[479076]
NPT2	Others	Unspecified		Activity	=	1.4	%	PMID[479078]
NPT2	Others	Unspecified		Ac50	n.a.	39.81	uM	PMID[479079]
NPT2	Others	Unspecified		AC50	n.a.	39810.7	nM	PMID[479079]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition index	=	-0.00104	n.a.	PMID[479080]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	20.97	%	PMID[479081]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Hit score	=	0.1779	n.a.	PMID[479082]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	12.99	%	PMID[479083]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	0.02	%	PMID[479084]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	20000.0	nM	PMID[479085]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	19952.62	nM	PMID[479085]
NPT2	Others	Unspecified		Potency	n.a.	298.5	nM	PubChem BioAssay data set

☑ 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 NPC180493 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	2077
0.1-0.2	33325
0.2-0.3	4177
0.3-0.4	2386
0.4-0.5	483
0.5-0.6	161
0.6-0.7	63
0.7-0.8	13
0.8-0.85	6
0.85-0.9	3
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9402	High Similarity	NPC109322
0.9035	High Similarity	NPC256849
0.887	High Similarity	NPC303899
0.8534	High Similarity	NPC47936
0.8279	Intermediate Similarity	NPC252603
0.8205	Intermediate Similarity	NPC75131
0.8049	Intermediate Similarity	NPC158847
0.7951	Intermediate Similarity	NPC148385
0.7823	Intermediate Similarity	NPC278549
0.7569	Intermediate Similarity	NPC321052
0.7536	Intermediate Similarity	NPC167285
0.7536	Intermediate Similarity	NPC226184
0.7536	Intermediate Similarity	NPC76544
0.744	Intermediate Similarity	NPC199790
0.7333	Intermediate Similarity	NPC476561
0.7154	Intermediate Similarity	NPC119133
0.7073	Intermediate Similarity	NPC476099
0.6935	Remote Similarity	NPC476562
0.6884	Remote Similarity	NPC246193
0.6855	Remote Similarity	NPC10466
0.6846	Remote Similarity	NPC326694
0.6667	Remote Similarity	NPC144223
0.6565	Remote Similarity	NPC41958
0.6408	Remote Similarity	NPC104011
0.6406	Remote Similarity	NPC476564
0.6301	Remote Similarity	NPC320818
0.6299	Remote Similarity	NPC174114
0.6299	Remote Similarity	NPC87981
0.6286	Remote Similarity	NPC248007
0.6242	Remote Similarity	NPC317821
0.6196	Remote Similarity	NPC325906
0.6174	Remote Similarity	NPC129756
0.6159	Remote Similarity	NPC327579
0.6144	Remote Similarity	NPC189068
0.6135	Remote Similarity	NPC324484
0.6104	Remote Similarity	NPC309832
0.6104	Remote Similarity	NPC219313
0.6081	Remote Similarity	NPC470140
0.6078	Remote Similarity	NPC107374
0.6078	Remote Similarity	NPC21448
0.6078	Remote Similarity	NPC156461
0.6071	Remote Similarity	NPC139776
0.6053	Remote Similarity	NPC229974
0.6045	Remote Similarity	NPC312187
0.6045	Remote Similarity	NPC4837
0.604	Remote Similarity	NPC470141
0.6039	Remote Similarity	NPC164665
0.6029	Remote Similarity	NPC313547
0.6024	Remote Similarity	NPC290959
0.6	Remote Similarity	NPC33996
0.6	Remote Similarity	NPC269827
0.5986	Remote Similarity	NPC57279
0.5969	Remote Similarity	NPC293163
0.596	Remote Similarity	NPC210947
0.596	Remote Similarity	NPC470139
0.5954	Remote Similarity	NPC317307
0.5954	Remote Similarity	NPC59314
0.5924	Remote Similarity	NPC136349
0.5921	Remote Similarity	NPC209525
0.5921	Remote Similarity	NPC161659
0.5918	Remote Similarity	NPC470138
0.5906	Remote Similarity	NPC126634
0.5878	Remote Similarity	NPC273327
0.5849	Remote Similarity	NPC211025
0.5849	Remote Similarity	NPC85689
0.5849	Remote Similarity	NPC185991
0.5844	Remote Similarity	NPC314152
0.5813	Remote Similarity	NPC321814
0.5813	Remote Similarity	NPC472816
0.5813	Remote Similarity	NPC207633
0.58	Remote Similarity	NPC262926
0.5789	Remote Similarity	NPC18335
0.5786	Remote Similarity	NPC150853
0.5776	Remote Similarity	NPC130586
0.5776	Remote Similarity	NPC212551
0.5776	Remote Similarity	NPC302778
0.5776	Remote Similarity	NPC164952
0.5767	Remote Similarity	NPC239737
0.5762	Remote Similarity	NPC61198
0.5759	Remote Similarity	NPC121222
0.5743	Remote Similarity	NPC287876
0.5741	Remote Similarity	NPC174802
0.5734	Remote Similarity	NPC470142
0.5714	Remote Similarity	NPC328479
0.5706	Remote Similarity	NPC52238
0.5706	Remote Similarity	NPC224076
0.5704	Remote Similarity	NPC180417
0.5676	Remote Similarity	NPC14330
0.5671	Remote Similarity	NPC311197
0.5671	Remote Similarity	NPC313754
0.5671	Remote Similarity	NPC226245
0.5671	Remote Similarity	NPC54320
0.5671	Remote Similarity	NPC316618
0.5652	Remote Similarity	NPC161224
0.565	Remote Similarity	NPC24589
0.5644	Remote Similarity	NPC60537
0.5636	Remote Similarity	NPC195140
0.5616	Remote Similarity	NPC15566
0.5613	Remote Similarity	NPC185903
0.5613	Remote Similarity	NPC286696
0.561	Remote Similarity	NPC472833

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 NPC180493 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	271
0.1-0.2	3411
0.2-0.3	2430
0.3-0.4	1934
0.4-0.5	781
0.5-0.6	221
0.6-0.7	64
0.7-0.8	17
0.8-0.85	7
0.85-0.9	4
0.9-0.95	9
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD78	Approved
1.0	High Similarity	NPD9544	Approved
0.925	High Similarity	NPD1128	Approved
0.925	High Similarity	NPD1127	Approved
0.9244	High Similarity	NPD281	Approved
0.906	High Similarity	NPD580	Discontinued
0.9035	High Similarity	NPD9358	Approved
0.9035	High Similarity	NPD9359	Approved
0.9024	High Similarity	NPD282	Approved
0.8908	High Similarity	NPD2221	Clinical (unspecified phase)
0.8655	High Similarity	NPD578	Discontinued
0.8594	High Similarity	NPD535	Approved
0.8548	High Similarity	NPD1775	Approved
0.8548	High Similarity	NPD1085	Approved
0.8537	High Similarity	NPD579	Clinical (unspecified phase)
0.8374	Intermediate Similarity	NPD4262	Discontinued
0.8372	Intermediate Similarity	NPD1119	Phase 2
0.8361	Intermediate Similarity	NPD9290	Approved
0.8279	Intermediate Similarity	NPD76	Approved
0.8279	Intermediate Similarity	NPD9289	Approved
0.8279	Intermediate Similarity	NPD9288	Approved
0.8279	Intermediate Similarity	NPD9292	Approved
0.8134	Intermediate Similarity	NPD2253	Discontinued
0.7971	Intermediate Similarity	NPD7531	Clinical (unspecified phase)
0.7951	Intermediate Similarity	NPD9086	Approved
0.781	Intermediate Similarity	NPD1117	Clinical (unspecified phase)
0.741	Intermediate Similarity	NPD1118	Discontinued
0.7339	Intermediate Similarity	NPD8954	Approved
0.7339	Intermediate Similarity	NPD8955	Approved
0.7154	Intermediate Similarity	NPD9291	Approved
0.7063	Intermediate Similarity	NPD2179	Discontinued
0.7039	Intermediate Similarity	NPD5321	Phase 3
0.6947	Remote Similarity	NPD9360	Approved
0.6824	Remote Similarity	NPD4183	Phase 3
0.6824	Remote Similarity	NPD4182	Phase 3
0.6715	Remote Similarity	NPD9408	Phase 3
0.6691	Remote Similarity	NPD9633	Phase 3
0.6689	Remote Similarity	NPD1730	Discontinued
0.6667	Remote Similarity	NPD4240	Approved
0.6667	Remote Similarity	NPD9626	Clinical (unspecified phase)
0.6623	Remote Similarity	NPD3708	Phase 2
0.6552	Remote Similarity	NPD1808	Phase 1
0.6528	Remote Similarity	NPD1120	Approved
0.6528	Remote Similarity	NPD1121	Approved
0.6485	Remote Similarity	NPD4155	Approved
0.6463	Remote Similarity	NPD3696	Approved
0.6463	Remote Similarity	NPD3695	Approved
0.6444	Remote Similarity	NPD237	Clinical (unspecified phase)
0.6429	Remote Similarity	NPD9605	Phase 3
0.6386	Remote Similarity	NPD3041	Approved
0.635	Remote Similarity	NPD9409	Discontinued
0.6343	Remote Similarity	NPD757	Phase 3
0.6316	Remote Similarity	NPD9373	Approved
0.6309	Remote Similarity	NPD1431	Approved
0.6309	Remote Similarity	NPD1430	Approved
0.6286	Remote Similarity	NPD9084	Phase 2
0.6277	Remote Similarity	NPD307	Approved
0.6268	Remote Similarity	NPD870	Clinical (unspecified phase)
0.6241	Remote Similarity	NPD4812	Phase 1
0.6222	Remote Similarity	NPD9374	Approved
0.6204	Remote Similarity	NPD9606	Approved
0.6196	Remote Similarity	NPD1776	Approved
0.6196	Remote Similarity	NPD1777	Approved
0.6181	Remote Similarity	NPD248	Discontinued
0.6159	Remote Similarity	NPD9607	Approved
0.6131	Remote Similarity	NPD1368	Approved
0.6119	Remote Similarity	NPD9375	Discontinued
0.6111	Remote Similarity	NPD3083	Approved
0.6078	Remote Similarity	NPD9627	Approved
0.6078	Remote Similarity	NPD249	Approved
0.6078	Remote Similarity	NPD7158	Phase 1
0.6078	Remote Similarity	NPD250	Approved
0.6051	Remote Similarity	NPD7842	Phase 2
0.6012	Remote Similarity	NPD3081	Clinical (unspecified phase)
0.6	Remote Similarity	NPD195	Approved
0.6	Remote Similarity	NPD1017	Clinical (unspecified phase)
0.6	Remote Similarity	NPD186	Discovery
0.5966	Remote Similarity	NPD1250	Clinical (unspecified phase)
0.5957	Remote Similarity	NPD1790	Clinical (unspecified phase)
0.5954	Remote Similarity	NPD8837	Clinical (unspecified phase)
0.5924	Remote Similarity	NPD548	Clinical (unspecified phase)
0.5921	Remote Similarity	NPD193	Suspended
0.5882	Remote Similarity	NPD5666	Phase 2
0.5875	Remote Similarity	NPD3107	Discontinued
0.5871	Remote Similarity	NPD171	Discontinued
0.587	Remote Similarity	NPD9584	Phase 2
0.5864	Remote Similarity	NPD2604	Approved
0.5862	Remote Similarity	NPD515	Phase 1
0.585	Remote Similarity	NPD9632	Phase 3
0.5849	Remote Similarity	NPD283	Approved
0.5844	Remote Similarity	NPD185	Approved
0.5839	Remote Similarity	NPD9083	Clinical (unspecified phase)
0.5839	Remote Similarity	NPD5340	Clinical (unspecified phase)
0.5789	Remote Similarity	NPD8836	Approved
0.5789	Remote Similarity	NPD3108	Clinical (unspecified phase)
0.5776	Remote Similarity	NPD1369	Phase 2
0.5776	Remote Similarity	NPD1750	Clinical (unspecified phase)
0.5776	Remote Similarity	NPD242	Approved
0.5776	Remote Similarity	NPD338	Approved
0.5772	Remote Similarity	NPD545	Clinical (unspecified phase)
0.5772	Remote Similarity	NPD547	Clinical (unspecified phase)
0.5769	Remote Similarity	NPD166	Approved
0.5767	Remote Similarity	NPD2646	Discontinued
0.5767	Remote Similarity	NPD2624	Phase 2
0.5766	Remote Similarity	NPD9082	Approved
0.5762	Remote Similarity	NPD252	Clinical (unspecified phase)
0.5753	Remote Similarity	NPD300	Approved
0.5744	Remote Similarity	NPD1623	Approved
0.5743	Remote Similarity	NPD8829	Clinical (unspecified phase)
0.5741	Remote Similarity	NPD339	Approved
0.5724	Remote Similarity	NPD2602	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD2191	Discontinued
0.5714	Remote Similarity	NPD549	Approved
0.5706	Remote Similarity	NPD169	Phase 2
0.5695	Remote Similarity	NPD194	Clinical (unspecified phase)
0.5679	Remote Similarity	NPD1731	Clinical (unspecified phase)
0.5679	Remote Similarity	NPD213	Clinical (unspecified phase)
0.5679	Remote Similarity	NPD214	Approved
0.5671	Remote Similarity	NPD1732	Phase 3
0.5671	Remote Similarity	NPD216	Approved
0.5671	Remote Similarity	NPD219	Phase 3
0.5671	Remote Similarity	NPD218	Approved
0.5671	Remote Similarity	NPD220	Clinical (unspecified phase)
0.5671	Remote Similarity	NPD217	Approved
0.5659	Remote Similarity	NPD9189	Discontinued
0.5655	Remote Similarity	NPD798	Discontinued
0.5644	Remote Similarity	NPD2180	Approved
0.5641	Remote Similarity	NPD1451	Approved
0.5638	Remote Similarity	NPD1705	Discontinued
0.5634	Remote Similarity	NPD8824	Phase 3
0.5629	Remote Similarity	NPD209	Clinical (unspecified phase)
0.5629	Remote Similarity	NPD1058	Discontinued
0.5613	Remote Similarity	NPD875	Clinical (unspecified phase)

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