NPASS Compound

Structure

NPC157173 OpenBabel07101719252D 31 32 0 0 1 0 0 0 0 0999 V2000 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 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 6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 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 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 2.5000 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 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 4.5000 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 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 4.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 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 4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 2 14 1 0 0 0 0 3 7 2 0 0 0 0 3 15 1 0 0 0 0 4 8 1 0 0 0 0 4 15 1 0 0 0 0 5 9 2 0 0 0 0 5 16 1 0 0 0 0 6 10 1 0 0 0 0 6 16 1 0 0 0 0 7 17 1 0 0 0 0 8 17 1 0 0 0 0 9 18 1 0 0 0 0 10 18 1 0 0 0 0 11 15 2 0 0 0 0 12 16 2 0 0 0 0 13 24 2 3 0 0 0 13 27 1 0 0 0 0 14 25 2 3 0 0 0 14 28 1 0 0 0 0 17 23 1 6 0 0 0 18 24 1 1 0 0 0 19 11 1 1 0 0 0 19 21 1 0 0 0 0 19 25 1 0 0 0 0 20 12 1 6 0 0 0 20 22 1 0 0 0 0 20 26 1 0 0 0 0 21 26 2 3 0 0 0 21 29 1 0 0 0 0 22 30 2 0 0 0 0 22 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	430.22
Volume:	438.802
LogP:	-0.773
LogD:	-0.18
LogS:	-1.271
# Rotatable Bonds:	9
TPSA:	150.95
# H-Bond Aceptor:	9
# H-Bond Donor:	5
# Rings:	2
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.37
Synthetic Accessibility Score:	4.2
Fsp3:	0.5
Lipinski Rule-of-5:	Accepted
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:	-5.838
MDCK Permeability:	6.467957518907497e-06
Pgp-inhibitor:	0.065
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.911
20% Bioavailability (F20%):	0.498
30% Bioavailability (F30%):	0.9

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.11
Plasma Protein Binding (PPB):	49.99268341064453%
Volume Distribution (VD):	0.431
Pgp-substrate:	42.59123992919922%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.069
CYP2C19-inhibitor:	0.057
CYP2C19-substrate:	0.047
CYP2C9-inhibitor:	0.033
CYP2C9-substrate:	0.111
CYP2D6-inhibitor:	0.027
CYP2D6-substrate:	0.192
CYP3A4-inhibitor:	0.012
CYP3A4-substrate:	0.134

ADMET: Excretion

Clearance (CL):	1.394
Half-life (T1/2):	0.816

ADMET: Toxicity

hERG Blockers:	0.048
Human Hepatotoxicity (H-HT):	0.907
Drug-inuced Liver Injury (DILI):	0.506
AMES Toxicity:	0.537
Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.939
Skin Sensitization:	0.945
Carcinogencity:	0.756
Eye Corrosion:	0.003
Eye Irritation:	0.033
Respiratory Toxicity:	0.141

Download Data

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

Natural Product: NPC157173

Natural Product ID:	NPC157173
*Common Name:**	Dehydroradiosumin
IUPAC Name:	n.a.
Synonyms:	Dehydroradiosumin
Standard InCHIKey:	ZKDJPRDXYUPPEK-UCINMQDPSA-N
Standard InCHI:	InChI=1S/C22H30N4O5/c1-13(27)24-18-9-5-16(6-10-18)12-20(22(30)31)26-21(29)19(25-14(2)28)11-15-3-7-17(23)8-4-15/h3,5,7,9,11-12,17-20H,4,6,8,10,23H2,1-2H3,(H,24,27)(H,25,28)(H,26,29)(H,30,31)/b15-11-,16-12-/t17-,18-,19-,20-/m0/s1
SMILES:	CC(=N[C@H]1C=C/C(=C/[C@@H](C(=O)O)N=C([C@H](/C=C2/C=C[C@@H](CC2)N)N=C(C)O)O)/CC1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL476077
PubChem CID:	11796882 44575446
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:0000348] Peptides [CHEMONTID:0004830] Dipeptides

*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
NPO2676	Anabaena cylindrica	Species	0stocaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9644086]
NPO2676	Anabaena cylindrica	Species	0stocaceae	Bacteria	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
IC50	2

Activity Type	# Activity
Individual Protein	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1720	Individual Protein	Plasminogen	Homo sapiens	IC50	=	90.0	ug.mL-1	PMID[566945]
NPT2	Others	Unspecified		IC50	=	0.1	ug.mL-1	PMID[566945]

☑ 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 NPC157173 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	48
0.1-0.2	1863
0.2-0.3	25256
0.3-0.4	12566
0.4-0.5	2541
0.5-0.6	400
0.6-0.7	22
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.6962	Remote Similarity	NPC60424
0.6962	Remote Similarity	NPC314221
0.6711	Remote Similarity	NPC325734
0.6667	Remote Similarity	NPC320057
0.6375	Remote Similarity	NPC316674
0.6321	Remote Similarity	NPC298484
0.6239	Remote Similarity	NPC474584
0.6238	Remote Similarity	NPC132931
0.6235	Remote Similarity	NPC133700
0.6214	Remote Similarity	NPC72401
0.6214	Remote Similarity	NPC325339
0.6196	Remote Similarity	NPC474312
0.6132	Remote Similarity	NPC327481
0.6118	Remote Similarity	NPC45060
0.6118	Remote Similarity	NPC280065
0.6076	Remote Similarity	NPC254541
0.6076	Remote Similarity	NPC320598
0.6055	Remote Similarity	NPC319579
0.6049	Remote Similarity	NPC273614
0.6024	Remote Similarity	NPC477525
0.6	Remote Similarity	NPC249713
0.5976	Remote Similarity	NPC77891
0.5949	Remote Similarity	NPC176164
0.5949	Remote Similarity	NPC189301
0.5941	Remote Similarity	NPC40663
0.5926	Remote Similarity	NPC6795
0.5875	Remote Similarity	NPC316826
0.5875	Remote Similarity	NPC327748
0.5875	Remote Similarity	NPC317143
0.5875	Remote Similarity	NPC321536
0.5875	Remote Similarity	NPC321468
0.587	Remote Similarity	NPC314854
0.587	Remote Similarity	NPC313911
0.5856	Remote Similarity	NPC329011
0.5849	Remote Similarity	NPC469895
0.5844	Remote Similarity	NPC321118
0.5844	Remote Similarity	NPC316889
0.5843	Remote Similarity	NPC78562
0.5843	Remote Similarity	NPC473588
0.5802	Remote Similarity	NPC327170
0.5802	Remote Similarity	NPC329564
0.5789	Remote Similarity	NPC197470
0.5784	Remote Similarity	NPC469739
0.5783	Remote Similarity	NPC182758
0.5776	Remote Similarity	NPC314992
0.5765	Remote Similarity	NPC113224
0.5765	Remote Similarity	NPC129995
0.5765	Remote Similarity	NPC315141
0.5761	Remote Similarity	NPC474833
0.5753	Remote Similarity	NPC297220
0.5739	Remote Similarity	NPC2265
0.573	Remote Similarity	NPC26932
0.573	Remote Similarity	NPC314678
0.5728	Remote Similarity	NPC175614
0.5701	Remote Similarity	NPC55336
0.5701	Remote Similarity	NPC164859
0.57	Remote Similarity	NPC236322
0.5696	Remote Similarity	NPC242930
0.5684	Remote Similarity	NPC224072
0.5679	Remote Similarity	NPC210999
0.5667	Remote Similarity	NPC35996
0.5663	Remote Similarity	NPC29468
0.566	Remote Similarity	NPC313234
0.5657	Remote Similarity	NPC316186
0.5656	Remote Similarity	NPC477937
0.5644	Remote Similarity	NPC319473
0.5641	Remote Similarity	NPC303672
0.5632	Remote Similarity	NPC474812
0.5632	Remote Similarity	NPC472579
0.5631	Remote Similarity	NPC189764
0.5625	Remote Similarity	NPC317147
0.5625	Remote Similarity	NPC318260
0.5619	Remote Similarity	NPC473364
0.5618	Remote Similarity	NPC315897
0.5614	Remote Similarity	NPC471645
0.5612	Remote Similarity	NPC202056
0.5612	Remote Similarity	NPC476141
0.561	Remote Similarity	NPC143722
0.561	Remote Similarity	NPC312826

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 NPC157173 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	51
0.1-0.2	325
0.2-0.3	4391
0.3-0.4	3623
0.4-0.5	675
0.5-0.6	85
0.6-0.7	0
0.7-0.8	0
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
0.6132	Remote Similarity	NPD2147	Approved
0.6	Remote Similarity	NPD2090	Approved
0.5849	Remote Similarity	NPD2258	Approved
0.5849	Remote Similarity	NPD2259	Approved
0.58	Remote Similarity	NPD1749	Approved
0.5795	Remote Similarity	NPD6944	Clinical (unspecified phase)
0.5789	Remote Similarity	NPD1348	Approved
0.5783	Remote Similarity	NPD9413	Discontinued
0.5776	Remote Similarity	NPD2217	Approved
0.5776	Remote Similarity	NPD2218	Phase 2
0.575	Remote Similarity	NPD9433	Approved
0.5743	Remote Similarity	NPD2251	Approved
0.5743	Remote Similarity	NPD2252	Approved
0.5741	Remote Similarity	NPD1040	Phase 2
0.5739	Remote Similarity	NPD2099	Approved
0.5726	Remote Similarity	NPD4504	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD1984	Approved
0.5698	Remote Similarity	NPD3709	Clinical (unspecified phase)
0.5641	Remote Similarity	NPD6093	Discontinued
0.563	Remote Similarity	NPD2956	Clinical (unspecified phase)
0.5618	Remote Similarity	NPD1825	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