NPASS Compound

Structure

CID314387 OpenBabel06191716122D 27 28 0 0 1 0 0 0 0 0999 V2000 -5.3563 2.4544 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 -1.9595 2.1637 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 -5.7631 1.5409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1753 0.7319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5116 0.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6808 1.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.1808 0.8364 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 3 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 0.8660 0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 1.4945 0.0000 N 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 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1 5 1 0 0 0 0 2 9 1 0 0 0 0 3 21 1 0 0 0 0 4 27 1 0 0 0 0 5 6 1 0 0 0 0 6 10 1 0 0 0 0 7 10 1 0 0 0 0 7 11 1 0 0 0 0 8 10 1 0 0 0 0 8 21 1 0 0 0 0 9 12 1 0 0 0 0 9 19 1 0 0 0 0 11 17 1 0 0 0 0 11 21 1 0 0 0 0 12 16 1 0 0 0 0 12 20 1 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 13 22 1 0 0 0 0 14 16 1 0 0 0 0 14 23 1 0 0 0 0 15 18 1 0 0 0 0 15 24 1 0 0 0 0 16 26 1 0 0 0 0 17 20 2 3 0 0 0 17 25 1 0 0 0 0 18 26 1 0 0 0 0 18 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Download Data

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

Natural Product: NPC314387

*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

☑ 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
EC50	3
Potency	6

Activity Type	# Activity
Individual Protein	3
NON-MOLECULAR	2
Organism	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1254	Individual Protein	Streptokinase A	Streptococcus pyogenes serotype M1	EC50	<	60.0	nM	PMID[523296]
NPT64	Individual Protein	ATPase family AAA domain-containing protein 5	Homo sapiens	Potency	n.a.	410.8	nM	PMID[523296]
NPT10	Individual Protein	Geminin	Homo sapiens	Potency	n.a.	6513.1	nM	PMID[523296]
NPT174	Organism	Streptococcus	Streptococcus	EC50	<	60.0	nM	PMID[523296]
NPT1252	Organism	Streptococcus sp. 'group A'	Streptococcus sp. 'group A'	EC50	<	60.0	nM	PMID[523296]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	2.9	nM	PMID[523296]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	82.8	nM	PMID[523296]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Potency	n.a.	47.3	nM	PMID[523297]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Potency	n.a.	94.3	nM	PMID[523297]

☑ 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 NPC314387 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	97
0.1-0.2	8004
0.2-0.3	20727
0.3-0.4	11963
0.4-0.5	1539
0.5-0.6	352
0.6-0.7	12
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9062	High Similarity	NPC313821
0.6296	Remote Similarity	NPC470284
0.6186	Remote Similarity	NPC475637
0.6186	Remote Similarity	NPC475127
0.6186	Remote Similarity	NPC473419
0.6186	Remote Similarity	NPC475715
0.6126	Remote Similarity	NPC208537
0.6126	Remote Similarity	NPC270005
0.6107	Remote Similarity	NPC470651
0.6107	Remote Similarity	NPC470655
0.6105	Remote Similarity	NPC233034
0.6082	Remote Similarity	NPC74555
0.6082	Remote Similarity	NPC306763
0.6082	Remote Similarity	NPC266242
0.6082	Remote Similarity	NPC254617
0.6082	Remote Similarity	NPC474469
0.6082	Remote Similarity	NPC126664
0.6082	Remote Similarity	NPC195165
0.6082	Remote Similarity	NPC34291
0.6075	Remote Similarity	NPC476523
0.6061	Remote Similarity	NPC477200
0.6053	Remote Similarity	NPC473597
0.6047	Remote Similarity	NPC50520
0.6018	Remote Similarity	NPC470283
0.5979	Remote Similarity	NPC184150
0.5979	Remote Similarity	NPC59221
0.5979	Remote Similarity	NPC141156
0.596	Remote Similarity	NPC163538
0.596	Remote Similarity	NPC115800
0.5918	Remote Similarity	NPC171850
0.5909	Remote Similarity	NPC52533
0.5888	Remote Similarity	NPC93630
0.5876	Remote Similarity	NPC294883
0.5876	Remote Similarity	NPC12514
0.5794	Remote Similarity	NPC288415
0.5794	Remote Similarity	NPC31313
0.5794	Remote Similarity	NPC45906
0.5794	Remote Similarity	NPC81006
0.5794	Remote Similarity	NPC149908
0.5776	Remote Similarity	NPC47076
0.5776	Remote Similarity	NPC134504
0.5755	Remote Similarity	NPC90839
0.5729	Remote Similarity	NPC145627
0.5714	Remote Similarity	NPC471202
0.5714	Remote Similarity	NPC325902
0.5714	Remote Similarity	NPC63191
0.5701	Remote Similarity	NPC471420
0.5686	Remote Similarity	NPC474468
0.5678	Remote Similarity	NPC220234
0.5676	Remote Similarity	NPC306838
0.567	Remote Similarity	NPC163134
0.567	Remote Similarity	NPC471419
0.566	Remote Similarity	NPC316807
0.5656	Remote Similarity	NPC471844
0.5644	Remote Similarity	NPC327753
0.5644	Remote Similarity	NPC327486
0.5644	Remote Similarity	NPC223174
0.5644	Remote Similarity	NPC473710
0.5644	Remote Similarity	NPC475694
0.5635	Remote Similarity	NPC478024
0.5631	Remote Similarity	NPC43219
0.5625	Remote Similarity	NPC470282
0.5619	Remote Similarity	NPC329077
0.561	Remote Similarity	NPC59589

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 NPC314387 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	62
0.1-0.2	1079
0.2-0.3	5166
0.3-0.4	2343
0.4-0.5	426
0.5-0.6	59
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	4
0.95-1	4

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD3185	Approved
1.0	High Similarity	NPD3184	Approved
1.0	High Similarity	NPD3182	Approved
1.0	High Similarity	NPD3183	Approved
0.9307	High Similarity	NPD3188	Approved
0.9062	High Similarity	NPD3190	Approved
0.9062	High Similarity	NPD3189	Approved
0.9062	High Similarity	NPD3191	Approved
0.8952	High Similarity	NPD7916	Approved
0.8952	High Similarity	NPD7915	Approved
0.619	Remote Similarity	NPD882	Phase 2
0.619	Remote Similarity	NPD883	Phase 2
0.6162	Remote Similarity	NPD3187	Discontinued
0.6105	Remote Similarity	NPD9440	Discontinued
0.6082	Remote Similarity	NPD9443	Clinical (unspecified phase)
0.6019	Remote Similarity	NPD3723	Clinical (unspecified phase)
0.5943	Remote Similarity	NPD2691	Clinical (unspecified phase)
0.5922	Remote Similarity	NPD372	Clinical (unspecified phase)
0.5887	Remote Similarity	NPD7914	Suspended
0.582	Remote Similarity	NPD8174	Phase 2
0.5766	Remote Similarity	NPD4759	Clinical (unspecified phase)
0.5758	Remote Similarity	NPD9444	Discontinued
0.5703	Remote Similarity	NPD7992	Clinical (unspecified phase)
0.569	Remote Similarity	NPD7844	Discontinued
0.5644	Remote Similarity	NPD9445	Approved
0.5614	Remote Similarity	NPD6943	Clinical (unspecified phase)
0.561	Remote Similarity	NPD8140	Approved
0.561	Remote Similarity	NPD8307	Discontinued
0.56	Remote Similarity	NPD4260	Discontinued

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