NPASS Compound

Structure

CID245534 OpenBabel06191716042D 30 31 0 0 1 0 0 0 0 0999 V2000 9.5263 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 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 2.0000 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 7.7942 1.5000 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 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 1 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 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 1 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 8.6603 3.0000 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 6.0622 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 3.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 3.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 2.0000 0.0000 N 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 4.3301 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 24 1 0 0 0 0 2 3 2 0 0 0 0 2 10 1 0 0 0 0 4 6 1 0 0 0 0 4 9 1 0 0 0 0 5 7 2 0 0 0 0 5 11 1 0 0 0 0 6 24 1 0 0 0 0 7 25 1 0 0 0 0 8 9 1 0 0 0 0 8 12 1 0 0 0 0 9 18 1 6 0 0 0 10 14 1 0 0 0 0 10 22 1 1 0 0 0 11 19 2 0 0 0 0 11 23 1 0 0 0 0 12 22 2 3 0 0 0 12 26 1 0 0 0 0 13 3 1 6 0 0 0 13 25 1 0 0 0 0 13 30 1 0 0 0 0 14 15 1 6 0 0 0 14 30 1 0 0 0 0 15 27 2 0 0 0 0 15 28 1 0 0 0 0 16 20 2 0 0 0 0 16 21 1 0 0 0 0 16 24 1 0 0 0 0 17 23 2 0 0 0 0 17 25 1 0 0 0 0 17 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	422.2
Volume:	398.945
LogP:	-3.841
LogD:	-1.831
LogS:	-1.82
# Rotatable Bonds:	10
TPSA:	216.4
# H-Bond Aceptor:	13
# H-Bond Donor:	9
# Rings:	2
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.136
Synthetic Accessibility Score:	4.796
Fsp3:	0.471
Lipinski Rule-of-5:	Rejected
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:	-6.833
MDCK Permeability:	0.0017336644232273102
Pgp-inhibitor:	0.0
Pgp-substrate:	0.985
Human Intestinal Absorption (HIA):	0.892
20% Bioavailability (F20%):	0.923
30% Bioavailability (F30%):	0.978

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.885
Plasma Protein Binding (PPB):	10.301311492919922%
Volume Distribution (VD):	0.458
Pgp-substrate:	82.71878051757812%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.051
CYP2C19-inhibitor:	0.04
CYP2C19-substrate:	0.035
CYP2C9-inhibitor:	0.166
CYP2C9-substrate:	0.014
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.171
CYP3A4-inhibitor:	0.004
CYP3A4-substrate:	0.009

ADMET: Excretion

Clearance (CL):	1.742
Half-life (T1/2):	0.78

ADMET: Toxicity

hERG Blockers:	0.043
Human Hepatotoxicity (H-HT):	0.853
Drug-inuced Liver Injury (DILI):	0.974
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.051
Skin Sensitization:	0.198
Carcinogencity:	0.047
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.052

Download Data

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

Natural Product: NPC245534

Natural Product ID:	NPC245534
*Common Name:**	Blasticidin_S
IUPAC Name:	(2S,3S,6R)-3-[[(3S)-3-amino-5-[carbamimidoyl(methyl)amino]pentanoyl]amino]-6-(4-amino-2-oxopyrimidin-1-yl)-3,6-dihydro-2H-pyran-2-carboxylic acid
Synonyms:	Blasticidin S
Standard InCHIKey:	CXNPLSGKWMLZPZ-ZNIXKSQXSA-N
Standard InCHI:	InChI=1S/C17H26N8O5/c1-24(16(20)21)6-4-9(18)8-12(26)22-10-2-3-13(30-14(10)15(27)28)25-7-5-11(19)23-17(25)29/h2-3,5,7,9-10,13-14H,4,6,8,18H2,1H3,(H3,20,21)(H,22,26)(H,27,28)(H2,19,23,29)/t9-,10-,13+,14-/m0/s1
SMILES:	N[C@H](CC(=N[C@H]1C=C[C@@H](O[C@@H]1C(=O)O)n1ccc(=N)nc1O)O)CCN(C(=N)N)C
Synthetic Gene Cluster:	BGC0000874;
ChEMBL Identifier:	CHEMBL476894
PubChem CID:	170012
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:0000347] Amino acids and derivatives [CHEMONTID:0001878] Beta amino acids and derivatives

*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
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[12964155]
NPO40484	Corticium sp.	Species	Corticiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1479383]
NPO40484	Corticium sp.	Species	Corticiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17391049]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19191560]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23377931]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	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
EC50	4
IC50	6
MIC	4
Others	7

Activity Type	# Activity
Organism	21

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	MIC	>	200.0	ug.mL-1	PMID[481015]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	EC50	=	13.0	ug.mL-1	PMID[481015]
NPT20	Organism	Candida albicans	Candida albicans	IC50	>	100.0	ug.mL-1	PMID[481016]
NPT20	Organism	Candida albicans	Candida albicans	IC50	=	6.0	ug.mL-1	PMID[481016]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	430.0	nM	PMID[481017]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	1150.0	nM	PMID[481017]
NPT3821	Organism	Alternaria citri	Alternaria citri	MIC	=	50.0	ug.mL-1	PMID[481018]
NPT3821	Organism	Alternaria citri	Alternaria citri	EC90	=	53.0	ug ml-1	PMID[481018]
NPT3660	Organism	Fusarium avenaceum	Fusarium avenaceum	MIC	=	25.0	ug.mL-1	PMID[481018]
NPT3660	Organism	Fusarium avenaceum	Fusarium avenaceum	EC90	=	7.0	ug ml-1	PMID[481018]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	MIC	>	200.0	ug.mL-1	PMID[481018]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	EC90	>	200.0	ug ml-1	PMID[481018]
NPT3821	Organism	Alternaria citri	Alternaria citri	EC50	=	6.0	ug.mL-1	PMID[481018]
NPT3660	Organism	Fusarium avenaceum	Fusarium avenaceum	EC50	=	0.4	ug.mL-1	PMID[481018]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	EC50	=	13.0	ug.mL-1	PMID[481018]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	Inhibition	=	25.2	%	PMID[481019]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	Inhibition	=	100.0	%	PMID[481019]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	Inhibition	=	76.6	%	PMID[481019]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	Activity	=	94.3	%	PMID[481019]

☑ 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 NPC245534 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	218
0.1-0.2	4709
0.2-0.3	28662
0.3-0.4	5980
0.4-0.5	2660
0.5-0.6	382
0.6-0.7	67
0.7-0.8	18
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
0.6486	Remote Similarity	NPC477519
0.6294	Remote Similarity	NPC318142
0.6259	Remote Similarity	NPC315058
0.6242	Remote Similarity	NPC319334
0.6242	Remote Similarity	NPC317377
0.6242	Remote Similarity	NPC322372
0.6242	Remote Similarity	NPC327517
0.6242	Remote Similarity	NPC321485
0.6242	Remote Similarity	NPC142761
0.6154	Remote Similarity	NPC261730
0.6127	Remote Similarity	NPC313962
0.6127	Remote Similarity	NPC469387
0.6119	Remote Similarity	NPC469423
0.6074	Remote Similarity	NPC313813
0.6068	Remote Similarity	NPC229249
0.605	Remote Similarity	NPC62927
0.605	Remote Similarity	NPC190334
0.595	Remote Similarity	NPC320057
0.5906	Remote Similarity	NPC328914
0.5906	Remote Similarity	NPC475758
0.5868	Remote Similarity	NPC328806
0.5859	Remote Similarity	NPC475791
0.5859	Remote Similarity	NPC13175
0.5827	Remote Similarity	NPC471261
0.5811	Remote Similarity	NPC471256
0.5794	Remote Similarity	NPC90240
0.5778	Remote Similarity	NPC147238
0.5769	Remote Similarity	NPC475149
0.5769	Remote Similarity	NPC471097
0.5766	Remote Similarity	NPC259586
0.576	Remote Similarity	NPC329384
0.5748	Remote Similarity	NPC328779
0.5746	Remote Similarity	NPC298484
0.5725	Remote Similarity	NPC470621
0.5725	Remote Similarity	NPC222481
0.5714	Remote Similarity	NPC6166
0.5714	Remote Similarity	NPC226769
0.5714	Remote Similarity	NPC280946
0.5714	Remote Similarity	NPC467022
0.5694	Remote Similarity	NPC471263
0.5691	Remote Similarity	NPC171116
0.5685	Remote Similarity	NPC324722
0.5685	Remote Similarity	NPC198644
0.5685	Remote Similarity	NPC311244
0.5682	Remote Similarity	NPC166242
0.5682	Remote Similarity	NPC322449
0.5682	Remote Similarity	NPC92874
0.5682	Remote Similarity	NPC62845
0.5682	Remote Similarity	NPC189854
0.5669	Remote Similarity	NPC120887
0.5669	Remote Similarity	NPC469424
0.5639	Remote Similarity	NPC471259
0.5639	Remote Similarity	NPC325900
0.5639	Remote Similarity	NPC10897
0.5625	Remote Similarity	NPC175614
0.5621	Remote Similarity	NPC81079
0.5606	Remote Similarity	NPC314413
0.5606	Remote Similarity	NPC314398
0.5606	Remote Similarity	NPC469895
0.5606	Remote Similarity	NPC239705

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 NPC245534 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	117
0.1-0.2	642
0.2-0.3	2468
0.3-0.4	3073
0.4-0.5	2078
0.5-0.6	674
0.6-0.7	71
0.7-0.8	26
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.719	Intermediate Similarity	NPD1428	Phase 2
0.696	Remote Similarity	NPD1805	Phase 2
0.696	Remote Similarity	NPD1804	Phase 2
0.6899	Remote Similarity	NPD6936	Clinical (unspecified phase)
0.6899	Remote Similarity	NPD6935	Phase 3
0.6822	Remote Similarity	NPD869	Approved
0.6741	Remote Similarity	NPD4816	Clinical (unspecified phase)
0.6718	Remote Similarity	NPD6918	Phase 1
0.6613	Remote Similarity	NPD4743	Phase 2
0.6555	Remote Similarity	NPD1706	Clinical (unspecified phase)
0.648	Remote Similarity	NPD3161	Clinical (unspecified phase)
0.6475	Remote Similarity	NPD192	Phase 2
0.64	Remote Similarity	NPD244	Clinical (unspecified phase)
0.6341	Remote Similarity	NPD3121	Phase 2
0.625	Remote Similarity	NPD285	Discontinued
0.6116	Remote Similarity	NPD9585	Discontinued
0.6068	Remote Similarity	NPD9601	Approved
0.605	Remote Similarity	NPD9603	Phase 3
0.605	Remote Similarity	NPD9604	Approved
0.605	Remote Similarity	NPD9602	Phase 3
0.6034	Remote Similarity	NPD9535	Phase 2
0.6034	Remote Similarity	NPD9534	Phase 2
0.6	Remote Similarity	NPD1385	Discontinued
0.6	Remote Similarity	NPD3138	Phase 3
0.5956	Remote Similarity	NPD3139	Phase 3
0.5948	Remote Similarity	NPD9600	Approved
0.5938	Remote Similarity	NPD7651	Approved
0.5906	Remote Similarity	NPD1455	Phase 3
0.5906	Remote Similarity	NPD1454	Phase 3
0.5902	Remote Similarity	NPD267	Discontinued
0.5902	Remote Similarity	NPD9565	Discontinued
0.5868	Remote Similarity	NPD9554	Approved
0.5868	Remote Similarity	NPD9553	Approved
0.5854	Remote Similarity	NPD6943	Clinical (unspecified phase)
0.5847	Remote Similarity	NPD9572	Clinical (unspecified phase)
0.5806	Remote Similarity	NPD1686	Approved
0.5794	Remote Similarity	NPD2621	Clinical (unspecified phase)
0.576	Remote Similarity	NPD215	Discontinued
0.5738	Remote Similarity	NPD301	Discontinued
0.5736	Remote Similarity	NPD2663	Approved
0.5726	Remote Similarity	NPD251	Approved
0.5725	Remote Similarity	NPD2633	Phase 1
0.5714	Remote Similarity	NPD6237	Clinical (unspecified phase)
0.5682	Remote Similarity	NPD6946	Approved
0.5672	Remote Similarity	NPD6693	Phase 3
0.5669	Remote Similarity	NPD514	Clinical (unspecified phase)
0.5667	Remote Similarity	NPD205	Approved
0.5649	Remote Similarity	NPD1061	Clinical (unspecified phase)
0.5643	Remote Similarity	NPD7756	Clinical (unspecified phase)
0.563	Remote Similarity	NPD9573	Phase 2
0.562	Remote Similarity	NPD9654	Phase 2
0.5606	Remote Similarity	NPD2258	Approved
0.5606	Remote Similarity	NPD2259	Approved
0.56	Remote Similarity	NPD6095	Approved
0.56	Remote Similarity	NPD6094	Approved

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