NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	181.06
Volume:	157.238
LogP:	-1.606
LogD:	-0.132
LogS:	-3.342
# Rotatable Bonds:	0
TPSA:	110.29
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	2
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.391
Synthetic Accessibility Score:	3.542
Fsp3:	0.167
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.082
MDCK Permeability:	8.513330249115825e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.979
Human Intestinal Absorption (HIA):	0.998
20% Bioavailability (F20%):	0.117
30% Bioavailability (F30%):	0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.197
Plasma Protein Binding (PPB):	18.150371551513672%
Volume Distribution (VD):	0.725
Pgp-substrate:	61.72119903564453%

ADMET: Metabolism

CYP1A2-inhibitor:	0.024
CYP1A2-substrate:	0.981
CYP2C19-inhibitor:	0.122
CYP2C19-substrate:	0.044
CYP2C9-inhibitor:	0.015
CYP2C9-substrate:	0.016
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.033
CYP3A4-inhibitor:	0.005
CYP3A4-substrate:	0.261

ADMET: Excretion

Clearance (CL):	6.608
Half-life (T1/2):	0.946

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.901
Drug-inuced Liver Injury (DILI):	0.979
AMES Toxicity:	0.025
Rat Oral Acute Toxicity:	0.881
Maximum Recommended Daily Dose:	0.017
Skin Sensitization:	0.109
Carcinogencity:	0.288
Eye Corrosion:	0.003
Eye Irritation:	0.221
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC476564

Natural Product ID:	NPC476564
*Common Name:**	6-Amino-9-methyl-1,7-dihydropurine-2,8-dione;hydrochloride
IUPAC Name:	6-amino-9-methyl-1,7-dihydropurine-2,8-dione;hydrochloride
Synonyms:
Standard InCHIKey:	HCXMOQBJSJPBLM-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C6H7N5O2.ClH/c1-11-4-2(8-6(11)13)3(7)9-5(12)10-4;/h1H3,(H,8,13)(H3,7,9,10,12);1H
SMILES:	CN1C2=NC(=O)NC(=C2NC1=O)N.Cl
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	46915512
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001797] Imidazopyrimidines [CHEMONTID:0000245] Purines and purine derivatives [CHEMONTID:0000597] Purinones

*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
NPO33243	Amphimedon sp.	Species	Niphatidae	Eukaryota	n.a.	Iojima Island, the Satsunan Islands, southern Japan (3047 N; 13017 E)	n.a.	PMID[15497958]
NPO33243	Amphimedon sp.	Species	Niphatidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17067172]
NPO33243	Amphimedon sp.	Species	Niphatidae	Eukaryota	n.a.	Republic of Palau	2006; 2007	PMID[20681583]
NPO33243	Amphimedon sp.	Species	Niphatidae	Eukaryota	n.a.	n.a.	n.a.	PMID[28207259]
NPO33243	Amphimedon sp.	Species	Niphatidae	Eukaryota	n.a.	n.a.	n.a.	PMID[7714542]
NPO33243	Amphimedon sp.	Species	Niphatidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9599281]

☑ 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
Others	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	18	nmol	PMID[20681583]

☑ 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 NPC476564 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	28649
0.1-0.2	9020
0.2-0.3	3255
0.3-0.4	1303
0.4-0.5	239
0.5-0.6	119
0.6-0.7	73
0.7-0.8	30
0.8-0.85	3
0.85-0.9	4
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9091	High Similarity	NPC87981
0.9091	High Similarity	NPC174114
0.8762	High Similarity	NPC4837
0.8762	High Similarity	NPC312187
0.8319	Intermediate Similarity	NPC139776
0.8286	Intermediate Similarity	NPC18335
0.8269	Intermediate Similarity	NPC476561
0.8103	Intermediate Similarity	NPC248007
0.8067	Intermediate Similarity	NPC104011
0.7778	Intermediate Similarity	NPC476562
0.7623	Intermediate Similarity	NPC246193
0.7623	Intermediate Similarity	NPC287876
0.7541	Intermediate Similarity	NPC14330
0.75	Intermediate Similarity	NPC68938
0.75	Intermediate Similarity	NPC189314
0.7479	Intermediate Similarity	NPC5707
0.7364	Intermediate Similarity	NPC317821
0.736	Intermediate Similarity	NPC57279
0.7344	Intermediate Similarity	NPC33996
0.7297	Intermediate Similarity	NPC476099
0.7287	Intermediate Similarity	NPC129756
0.7231	Intermediate Similarity	NPC161659
0.7231	Intermediate Similarity	NPC209525
0.7155	Intermediate Similarity	NPC303899
0.7121	Intermediate Similarity	NPC314152
0.7121	Intermediate Similarity	NPC229974
0.7105	Intermediate Similarity	NPC75131
0.709	Intermediate Similarity	NPC164665
0.709	Intermediate Similarity	NPC189068
0.7037	Intermediate Similarity	NPC219313
0.7037	Intermediate Similarity	NPC309832
0.7015	Intermediate Similarity	NPC21448
0.7015	Intermediate Similarity	NPC107374
0.7015	Intermediate Similarity	NPC156461
0.6934	Remote Similarity	NPC136349
0.6912	Remote Similarity	NPC269827
0.6903	Remote Similarity	NPC10466
0.6861	Remote Similarity	NPC121222
0.686	Remote Similarity	NPC158847
0.6838	Remote Similarity	NPC47936
0.6807	Remote Similarity	NPC199790
0.6767	Remote Similarity	NPC296437
0.6763	Remote Similarity	NPC150853
0.6723	Remote Similarity	NPC256849
0.6716	Remote Similarity	NPC470266
0.6714	Remote Similarity	NPC161224
0.6714	Remote Similarity	NPC85689
0.6714	Remote Similarity	NPC211025
0.6714	Remote Similarity	NPC185991
0.6667	Remote Similarity	NPC472816
0.6667	Remote Similarity	NPC328479
0.6667	Remote Similarity	NPC321814
0.6639	Remote Similarity	NPC278549
0.6638	Remote Similarity	NPC119133
0.662	Remote Similarity	NPC212551
0.662	Remote Similarity	NPC164952
0.662	Remote Similarity	NPC130586
0.662	Remote Similarity	NPC302778
0.6618	Remote Similarity	NPC476528
0.6618	Remote Similarity	NPC476433
0.6612	Remote Similarity	NPC148385
0.6597	Remote Similarity	NPC239737
0.6573	Remote Similarity	NPC174802
0.6573	Remote Similarity	NPC472834
0.6569	Remote Similarity	NPC476522
0.6569	Remote Similarity	NPC476013
0.6569	Remote Similarity	NPC474986
0.6569	Remote Similarity	NPC476520
0.6569	Remote Similarity	NPC217656
0.6552	Remote Similarity	NPC195140
0.6547	Remote Similarity	NPC476408
0.6532	Remote Similarity	NPC252603
0.6528	Remote Similarity	NPC224076
0.6522	Remote Similarity	NPC89139
0.6522	Remote Similarity	NPC476521
0.6491	Remote Similarity	NPC293163
0.6483	Remote Similarity	NPC226245
0.6483	Remote Similarity	NPC316618
0.6483	Remote Similarity	NPC93365
0.6466	Remote Similarity	NPC59314
0.646	Remote Similarity	NPC320256
0.6457	Remote Similarity	NPC109322
0.6446	Remote Similarity	NPC41958
0.6434	Remote Similarity	NPC207633
0.6414	Remote Similarity	NPC52238
0.6406	Remote Similarity	NPC180493
0.6383	Remote Similarity	NPC244700
0.637	Remote Similarity	NPC54320
0.637	Remote Similarity	NPC311197
0.637	Remote Similarity	NPC313754
0.6339	Remote Similarity	NPC51000
0.6301	Remote Similarity	NPC472833
0.6291	Remote Similarity	NPC325906
0.6267	Remote Similarity	NPC323091
0.6225	Remote Similarity	NPC324484
0.6174	Remote Similarity	NPC472832
0.6174	Remote Similarity	NPC18308
0.6142	Remote Similarity	NPC327579
0.6104	Remote Similarity	NPC290959
0.6104	Remote Similarity	NPC326082
0.6102	Remote Similarity	NPC273327
0.6078	Remote Similarity	NPC261595
0.6058	Remote Similarity	NPC320818
0.6039	Remote Similarity	NPC324033
0.6039	Remote Similarity	NPC321458
0.6013	Remote Similarity	NPC189261
0.6	Remote Similarity	NPC313547
0.5949	Remote Similarity	NPC326529
0.5912	Remote Similarity	NPC164845
0.5912	Remote Similarity	NPC324198
0.5912	Remote Similarity	NPC319100
0.5882	Remote Similarity	NPC187191
0.5882	Remote Similarity	NPC326248
0.587	Remote Similarity	NPC321929
0.5849	Remote Similarity	NPC313897
0.582	Remote Similarity	NPC163105
0.5793	Remote Similarity	NPC24589
0.5758	Remote Similarity	NPC265111
0.5726	Remote Similarity	NPC9639
0.5725	Remote Similarity	NPC324009
0.5706	Remote Similarity	NPC473585
0.5702	Remote Similarity	NPC75844
0.5689	Remote Similarity	NPC282458
0.5689	Remote Similarity	NPC78941
0.5683	Remote Similarity	NPC319221
0.5625	Remote Similarity	NPC327613
0.5615	Remote Similarity	NPC240084
0.5614	Remote Similarity	NPC326364
0.56	Remote Similarity	NPC27699

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 NPC476564 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1166
0.1-0.2	3545
0.2-0.3	2193
0.3-0.4	1432
0.4-0.5	565
0.5-0.6	146
0.6-0.7	80
0.7-0.8	23
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8286	Intermediate Similarity	NPD8836	Approved
0.8103	Intermediate Similarity	NPD9084	Phase 2
0.7881	Intermediate Similarity	NPD9408	Phase 3
0.7833	Intermediate Similarity	NPD9633	Phase 3
0.775	Intermediate Similarity	NPD870	Clinical (unspecified phase)
0.7623	Intermediate Similarity	NPD248	Discontinued
0.7623	Intermediate Similarity	NPD8829	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD8833	Approved
0.75	Intermediate Similarity	NPD8831	Approved
0.7479	Intermediate Similarity	NPD8830	Phase 3
0.744	Intermediate Similarity	NPD9083	Clinical (unspecified phase)
0.7231	Intermediate Similarity	NPD193	Suspended
0.7121	Intermediate Similarity	NPD185	Approved
0.7109	Intermediate Similarity	NPD9484	Clinical (unspecified phase)
0.7099	Intermediate Similarity	NPD3695	Approved
0.7099	Intermediate Similarity	NPD3696	Approved
0.7031	Intermediate Similarity	NPD1058	Discontinued
0.7015	Intermediate Similarity	NPD250	Approved
0.7015	Intermediate Similarity	NPD166	Approved
0.7015	Intermediate Similarity	NPD249	Approved
0.7015	Intermediate Similarity	NPD7158	Phase 1
0.694	Remote Similarity	NPD4240	Approved
0.6934	Remote Similarity	NPD548	Clinical (unspecified phase)
0.6912	Remote Similarity	NPD195	Approved
0.6912	Remote Similarity	NPD186	Discovery
0.6891	Remote Similarity	NPD757	Phase 3
0.6889	Remote Similarity	NPD171	Discontinued
0.6884	Remote Similarity	NPD3708	Phase 2
0.6838	Remote Similarity	NPD1730	Discontinued
0.6818	Remote Similarity	NPD799	Phase 1
0.6815	Remote Similarity	NPD9704	Approved
0.6738	Remote Similarity	NPD3107	Discontinued
0.6723	Remote Similarity	NPD9359	Approved
0.6723	Remote Similarity	NPD9358	Approved
0.6714	Remote Similarity	NPD283	Approved
0.6638	Remote Similarity	NPD9291	Approved
0.662	Remote Similarity	NPD338	Approved
0.662	Remote Similarity	NPD1369	Phase 2
0.662	Remote Similarity	NPD242	Approved
0.662	Remote Similarity	NPD1750	Clinical (unspecified phase)
0.6597	Remote Similarity	NPD2624	Phase 2
0.6597	Remote Similarity	NPD2646	Discontinued
0.6573	Remote Similarity	NPD339	Approved
0.6532	Remote Similarity	NPD76	Approved
0.6532	Remote Similarity	NPD9289	Approved
0.6532	Remote Similarity	NPD9288	Approved
0.6532	Remote Similarity	NPD9292	Approved
0.6528	Remote Similarity	NPD169	Phase 2
0.6503	Remote Similarity	NPD214	Approved
0.6503	Remote Similarity	NPD213	Clinical (unspecified phase)
0.6483	Remote Similarity	NPD1732	Phase 3
0.6483	Remote Similarity	NPD546	Clinical (unspecified phase)
0.6475	Remote Similarity	NPD9086	Approved
0.6466	Remote Similarity	NPD8837	Clinical (unspecified phase)
0.6452	Remote Similarity	NPD578	Discontinued
0.6446	Remote Similarity	NPD9373	Approved
0.6406	Remote Similarity	NPD9544	Approved
0.6406	Remote Similarity	NPD78	Approved
0.64	Remote Similarity	NPD580	Discontinued
0.6378	Remote Similarity	NPD4262	Discontinued
0.637	Remote Similarity	NPD220	Clinical (unspecified phase)
0.637	Remote Similarity	NPD216	Approved
0.637	Remote Similarity	NPD219	Phase 3
0.637	Remote Similarity	NPD218	Approved
0.637	Remote Similarity	NPD217	Approved
0.6357	Remote Similarity	NPD281	Approved
0.6351	Remote Similarity	NPD516	Clinical (unspecified phase)
0.6341	Remote Similarity	NPD9374	Approved
0.6339	Remote Similarity	NPD8838	Approved
0.6308	Remote Similarity	NPD9696	Approved
0.6299	Remote Similarity	NPD2221	Clinical (unspecified phase)
0.6291	Remote Similarity	NPD1777	Approved
0.6291	Remote Similarity	NPD1776	Approved
0.6291	Remote Similarity	NPD7988	Suspended
0.6279	Remote Similarity	NPD579	Clinical (unspecified phase)
0.6271	Remote Similarity	NPD9626	Clinical (unspecified phase)
0.626	Remote Similarity	NPD1128	Approved
0.626	Remote Similarity	NPD1127	Approved
0.625	Remote Similarity	NPD6112	Approved
0.623	Remote Similarity	NPD9375	Discontinued
0.619	Remote Similarity	NPD9606	Approved
0.619	Remote Similarity	NPD9360	Approved
0.6148	Remote Similarity	NPD8955	Approved
0.6148	Remote Similarity	NPD8954	Approved
0.6144	Remote Similarity	NPD2647	Phase 3
0.6142	Remote Similarity	NPD307	Approved
0.6142	Remote Similarity	NPD9607	Approved
0.6126	Remote Similarity	NPD8565	Clinical (unspecified phase)
0.6119	Remote Similarity	NPD282	Approved
0.6094	Remote Similarity	NPD9409	Discontinued
0.6093	Remote Similarity	NPD3083	Approved
0.6093	Remote Similarity	NPD2593	Clinical (unspecified phase)
0.6078	Remote Similarity	NPD247	Clinical (unspecified phase)
0.6063	Remote Similarity	NPD237	Clinical (unspecified phase)
0.6061	Remote Similarity	NPD1775	Approved
0.6061	Remote Similarity	NPD1085	Approved
0.6051	Remote Similarity	NPD5666	Phase 2
0.6014	Remote Similarity	NPD9550	Approved
0.6014	Remote Similarity	NPD9551	Approved
0.6	Remote Similarity	NPD306	Approved
0.5985	Remote Similarity	NPD1119	Phase 2
0.5975	Remote Similarity	NPD1412	Clinical (unspecified phase)
0.5935	Remote Similarity	NPD1215	Discontinued
0.5912	Remote Similarity	NPD4171	Clinical (unspecified phase)
0.5887	Remote Similarity	NPD1118	Discontinued
0.587	Remote Similarity	NPD8827	Approved
0.5852	Remote Similarity	NPD9571	Approved
0.5821	Remote Similarity	NPD9366	Approved
0.5821	Remote Similarity	NPD515	Phase 1
0.5804	Remote Similarity	NPD1117	Clinical (unspecified phase)
0.5802	Remote Similarity	NPD4716	Approved
0.5793	Remote Similarity	NPD1692	Approved
0.5772	Remote Similarity	NPD1816	Clinical (unspecified phase)
0.5767	Remote Similarity	NPD4744	Clinical (unspecified phase)
0.5753	Remote Similarity	NPD7531	Clinical (unspecified phase)
0.5734	Remote Similarity	NPD2253	Discontinued
0.5725	Remote Similarity	NPD9290	Approved
0.5723	Remote Similarity	NPD5684	Clinical (unspecified phase)
0.5723	Remote Similarity	NPD6417	Clinical (unspecified phase)
0.5723	Remote Similarity	NPD5683	Clinical (unspecified phase)
0.5723	Remote Similarity	NPD5682	Phase 3
0.5714	Remote Similarity	NPD9194	Approved
0.5714	Remote Similarity	NPD535	Approved
0.5714	Remote Similarity	NPD9193	Approved
0.5704	Remote Similarity	NPD8826	Approved
0.5702	Remote Similarity	NPD8566	Approved
0.5697	Remote Similarity	NPD2457	Phase 2
0.5697	Remote Similarity	NPD2456	Phase 2
0.5695	Remote Similarity	NPD2128	Phase 1
0.5655	Remote Similarity	NPD2632	Approved
0.5655	Remote Similarity	NPD2630	Approved
0.5655	Remote Similarity	NPD2631	Clinical (unspecified phase)
0.5614	Remote Similarity	NPD9103	Approved
0.5614	Remote Similarity	NPD9102	Approved
0.5612	Remote Similarity	NPD545	Clinical (unspecified phase)
0.5612	Remote Similarity	NPD547	Clinical (unspecified phase)
0.5603	Remote Similarity	NPD1121	Approved
0.5603	Remote Similarity	NPD1120	Approved
0.56	Remote Similarity	NPD8571	Phase 3
0.56	Remote Similarity	NPD9071	Phase 3

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