NPASS Compound

Structure

NPC484440 OpenBabel06302215132D 39 43 0 0 0 0 0 0 0 0999 V2000 5.7510 2.7338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2510 3.5998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2564 3.7044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5873 2.9612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6092 3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1340 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1340 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2079 3.9781 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.2024 4.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7024 4.9487 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 0.0000 O 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 -0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0000 -1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0000 -1.7321 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 4.0485 4.6825 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.9146 5.1825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0191 6.1770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6577 4.5134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6359 4.7213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3050 3.9781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9449 5.6723 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.2757 6.4155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5848 7.3666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5629 7.5745 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.8719 8.5255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2320 6.8313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9230 5.8803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 30 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 27 1 0 0 0 0 4 5 2 0 0 0 0 5 13 1 0 0 0 0 5 6 1 0 0 0 0 6 11 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 15 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 15 16 2 0 0 0 0 15 17 2 0 0 0 0 15 18 1 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 28 30 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 33 39 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 36 38 1 0 0 0 0 38 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	430.21
Volume:	419.214
LogP:	1.752
LogD:	1.136
LogS:	-5.456
# Rotatable Bonds:	4
TPSA:	93.22
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.624
Synthetic Accessibility Score:	5.954
Fsp3:	0.826
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:	-5.253
MDCK Permeability:	2.118922748195473e-05
Pgp-inhibitor:	0.958
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.969
30% Bioavailability (F30%):	0.958

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.897
Plasma Protein Binding (PPB):	15.060832023620605%
Volume Distribution (VD):	0.928
Pgp-substrate:	72.1238784790039%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.932
CYP2C19-inhibitor:	0.054
CYP2C19-substrate:	0.94
CYP2C9-inhibitor:	0.162
CYP2C9-substrate:	0.042
CYP2D6-inhibitor:	0.031
CYP2D6-substrate:	0.023
CYP3A4-inhibitor:	0.392
CYP3A4-substrate:	0.92

ADMET: Excretion

Clearance (CL):	11.427
Half-life (T1/2):	0.204

ADMET: Toxicity

hERG Blockers:	0.06
Human Hepatotoxicity (H-HT):	0.247
Drug-inuced Liver Injury (DILI):	0.067
AMES Toxicity:	0.234
Rat Oral Acute Toxicity:	0.857
Maximum Recommended Daily Dose:	0.937
Skin Sensitization:	0.606
Carcinogencity:	0.238
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.057

Download Data

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

Natural Product: NPC484440

Natural Product ID:	NPC484440
*Common Name:**	FPYJSJDOHRDAMT-KQWNVCNZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FPYJSJDOHRDAMT-KQWNVCNZSA-N
Standard InCHI:	InChI=1S/C28H30ClN5O4S/c1-17-25(30-18(2)26(17)28(36)34-12-10-32(3)11-13-34)16-23-22-15-21(8-9-24(22)31-27(23)35)39(37,38)33(4)20-7-5-6-19(29)14-20/h5-9,14-16,30H,10-13H2,1-4H3,(H,31,35)/b23-16-
SMILES:	Cc1c(/C=C2/c3cc(ccc3N=C2O)S(=O)(=O)N(C)c2cccc(c2)Cl)[nH]c(C)c1C(=O)N1CCN(C)CC1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	9549297
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000038] Sulfanilides

*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
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1367520]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15974609]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[21381678]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21667925]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22118684]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26692349]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33089690]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8626236]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	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
IC50	26
Ki	3
Others	10

Activity Type	# Activity
Cell Line	12
CELL-LINE	2
Individual Protein	13
Organism	10
Protein Complex	1
SINGLE PROTEIN	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1337	Individual Protein	Hepatocyte growth factor receptor	Homo sapiens	IC50	=	20.0	nM	PMID[18077363]
NPT1337	Individual Protein	Hepatocyte growth factor receptor	Homo sapiens	IC50	=	14.0	nM	PMID[21405128]
NPT6374	Cell Line	BaF3	Mus musculus	IC50	=	530.0	nM	PMID[21405128]
NPT6374	Cell Line	BaF3	Mus musculus	IC50	=	6400.0	nM	PMID[21405128]
NPT886	Cell Line	NIH3T3	Mus musculus	IC50	=	2000.0	nM	PMID[21405128]
NPT886	Cell Line	NIH3T3	Mus musculus	IC50	>=	50000.0	nM	PMID[21405128]
NPT1097	Cell Line	MKN-45	Homo sapiens	IC50	=	1300.0	nM	PMID[21405128]
NPT2353	Cell Line	NCI-H1993	Homo sapiens	IC50	=	7300.0	nM	PMID[21405128]
NPT2091	Cell Line	SNU-5	Homo sapiens	IC50	=	800.0	nM	PMID[21405128]
NPT788	Cell Line	SNU1	Homo sapiens	IC50	=	7000.0	nM	PMID[21405128]
NPT2476	Cell Line	NCI-H441	Homo sapiens	IC50	=	13000.0	nM	PMID[21405128]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	11000.0	nM	PMID[21405128]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	6200.0	nM	PMID[21405128]
NPT1081	Cell Line	BXPC-3	Homo sapiens	IC50	=	16000.0	nM	PMID[21405128]
NPT1337	Individual Protein	Hepatocyte growth factor receptor	Homo sapiens	IC50	=	20.0	nM	PMID[21641696]
NPT1337	Individual Protein	Hepatocyte growth factor receptor	Homo sapiens	IC50	=	10.0	nM	PMID[21812414]
NPT1337	Individual Protein	Hepatocyte growth factor receptor	Homo sapiens	IC50	=	152.0	nM	PMID[22138308]
NPT1337	Individual Protein	Hepatocyte growth factor receptor	Homo sapiens	IC50	=	1561.0	nM	PMID[22138308]
NPT1337	Individual Protein	Hepatocyte growth factor receptor	Homo sapiens	IC50	=	228.0	nM	PMID[22138308]
NPT1337	Individual Protein	Hepatocyte growth factor receptor	Homo sapiens	Inhibition	=	61.8	%	PMID[22130133]
NPT3390	Individual Protein	Macrophage-stimulating protein receptor	Homo sapiens	Inhibition	=	52.2	%	PMID[22130133]
NPT3259	Individual Protein	Tyrosine-protein kinase ZAP-70	Homo sapiens	Ki	>	10000.0	nM	PMID[22289061]
NPT3263	Individual Protein	Protein tyrosine kinase 2 beta	Homo sapiens	Ki	=	10.47	nM	PMID[22289061]
NPT6368	Individual Protein	Hepatocyte growth factor receptor	Canis familiaris	IC50	=	200.0	nM	PMID[22738633]
NPT1337	Individual Protein	Hepatocyte growth factor receptor	Homo sapiens	Inhibition	=	70.0	%	PMID[26692349]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Inhibition	=	85.07	%	PMID[19666223]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	320.0	nM	PMID[19666223]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	228.0	nM	PMID[19666223]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	620.0	nM	PMID[19666223]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	317.0	nM	PMID[19666223]
NPT3944	Protein Complex	Cyclin-dependent kinase 2/cyclin E1	Homo sapiens	Ki	=	489.78	nM	PMID[22289061]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-0.18	%	DOI[10.21203/rs.3.rs-23951/v1]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	4.722	%	DOI[10.6019/CHEMBL4495564]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	1.22	%	DOI[10.6019/CHEMBL4495565]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	=	10870.0	nM	DOI[10.6019/CHEMBL4495565]
NPT22224	CELL-LINE	Vero C1008	Chlorocebus sabaeus	CC50	=	10420.0	nM	DOI[10.6019/CHEMBL4495565]

☑ 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 NPC484440 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	434
0.1-0.2	3936
0.2-0.3	14583
0.3-0.4	17239
0.4-0.5	2852
0.5-0.6	2953
0.6-0.7	699
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

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 NPC484440 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	224
0.1-0.2	639
0.2-0.3	967
0.3-0.4	1876
0.4-0.5	2636
0.5-0.6	2397
0.6-0.7	407
0.7-0.8	4
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

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