NPASS Compound

Structure

CID244509 OpenBabel06191716042D 54 56 0 0 1 0 0 0 0 0999 V2000 -5.7737 2.0536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4209 0.1515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1336 0.4096 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8728 -2.4360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9059 3.8556 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7765 2.1284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6374 4.0321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5034 5.5321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5034 3.5321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3694 5.0321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9620 6.5470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6672 7.5026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0537 1.7638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4361 -0.7453 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7713 5.5321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3454 3.1041 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 6.6720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1638 -0.9865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4531 -0.2433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2028 0.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7238 -1.4471 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3426 3.0293 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.6374 5.0321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1229 2.1291 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.3694 4.0321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2818 5.8140 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.9053 5.0321 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8898 0.5829 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9888 0.1490 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3474 8.2356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 6.6720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3454 3.1041 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2818 5.8140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9053 5.0321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8898 0.5829 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1229 2.1291 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9888 0.1490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0526 9.1912 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.2706 4.1013 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.4556 6.3773 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.6229 1.2631 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.4556 6.3773 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.6229 1.2631 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.2706 4.1013 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 -2.0192 -1.1443 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2354 3.5321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3223 8.0131 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6490 7.6609 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9620 6.5470 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7713 5.5321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4531 -0.2433 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0537 1.7638 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2836 -0.8065 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 1 0 0 0 0 2 20 1 0 0 0 0 3 20 1 0 0 0 0 6 22 1 0 0 0 0 7 9 1 0 0 0 0 7 23 2 0 0 0 0 8 10 2 0 0 0 0 8 23 1 0 0 0 0 9 25 2 0 0 0 0 10 25 1 0 0 0 0 11 12 1 0 0 0 0 12 30 1 0 0 0 0 13 20 1 0 0 0 0 14 21 1 0 0 0 0 15 23 1 0 0 0 0 16 24 1 0 0 0 0 16 39 2 0 0 0 0 17 31 1 0 0 0 0 17 40 1 0 0 0 0 18 21 1 0 0 0 0 18 45 1 0 0 0 0 19 46 1 0 0 0 0 21 4 1 6 0 0 0 22 5 1 6 0 0 0 24 13 1 6 0 0 0 24 41 1 0 0 0 0 25 47 1 0 0 0 0 26 11 1 1 0 0 0 26 34 1 0 0 0 0 26 42 1 0 0 0 0 27 15 1 6 0 0 0 27 33 1 0 0 0 0 27 39 1 0 0 0 0 28 19 1 6 0 0 0 28 37 1 0 0 0 0 28 43 1 0 0 0 0 29 14 1 6 0 0 0 29 35 1 0 0 0 0 29 45 1 0 0 0 0 30 38 2 0 0 0 0 30 48 1 0 0 0 0 31 42 2 3 0 0 0 31 49 1 0 0 0 0 32 22 1 6 0 0 0 32 36 1 0 0 0 0 32 44 1 0 0 0 0 33 40 2 3 0 0 0 33 50 1 0 0 0 0 34 44 2 3 0 0 0 34 51 1 0 0 0 0 35 41 2 3 0 0 0 35 52 1 0 0 0 0 36 43 2 3 0 0 0 36 53 1 0 0 0 0 37 45 1 0 0 0 0 37 54 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	756.42
Volume:	760.924
LogP:	0.555
LogD:	1.322
LogS:	-2.434
# Rotatable Bonds:	10
TPSA:	266.2
# H-Bond Aceptor:	17
# H-Bond Donor:	9
# Rings:	3
# Heavy Atoms:	17

MedChem Properties

QED Drug-Likeness Score:	0.121
Synthetic Accessibility Score:	6.097
Fsp3:	0.622
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.457
MDCK Permeability:	9.749443415785208e-05
Pgp-inhibitor:	0.014
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.983
20% Bioavailability (F20%):	0.926
30% Bioavailability (F30%):	0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.045
Plasma Protein Binding (PPB):	43.82403564453125%
Volume Distribution (VD):	0.472
Pgp-substrate:	51.94246292114258%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.012
CYP2C19-inhibitor:	0.046
CYP2C19-substrate:	0.042
CYP2C9-inhibitor:	0.046
CYP2C9-substrate:	0.28
CYP2D6-inhibitor:	0.035
CYP2D6-substrate:	0.101
CYP3A4-inhibitor:	0.072
CYP3A4-substrate:	0.014

ADMET: Excretion

Clearance (CL):	1.962
Half-life (T1/2):	0.873

ADMET: Toxicity

hERG Blockers:	0.004
Human Hepatotoxicity (H-HT):	0.999
Drug-inuced Liver Injury (DILI):	0.931
AMES Toxicity:	0.014
Rat Oral Acute Toxicity:	0.137
Maximum Recommended Daily Dose:	0.954
Skin Sensitization:	0.775
Carcinogencity:	0.371
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.94

Download Data

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

Natural Product: NPC244509

Natural Product ID:	NPC244509
*Common Name:**	Nostocyclopeptide A1
IUPAC Name:	n.a.
Synonyms:	nostocyclopeptide A1
Standard InCHIKey:	TZHROWIOAVYSMP-DOPKCXIESA-N
Standard InCHI:	InChI=1S/C37H56N8O9/c1-6-22(5)32-36(53)43-28(19-46)37(54)45-18-21(4)14-29(45)35(52)41-24(13-20(2)3)16-39-27(15-23-7-9-25(47)10-8-23)33(50)40-17-31(49)42-26(34(51)44-32)11-12-30(38)48/h7-10,16,20-22,24,26-29,32,46-47H,6,11-15,17-19H2,1-5H3,(H2,38,48)(H,40,50)(H,41,52)(H,42,49)(H,43,53)(H,44,51)/b39-16+/t21-,22-,24-,26+,27-,28-,29-,32-/m0/s1
SMILES:	CC[C@H](C)[C@H]1C(=N[C@@H](CO)C(=O)N2C[C@@H](C)C[C@H]2C(=N[C@@H](CC(C)C)/C=N/[C@@H](Cc2ccc(cc2)O)C(=NCC(=N[C@H](CCC(=N)O)C(=N1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL451336
PubChem CID:	NA
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:0004831] Oligopeptides

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24476550]
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO8945	Grevillea robusta	Species	Proteaceae	Eukaryota	leaves	n.a.	n.a.	PMID[17243726]
NPO4541	Capnella lacertiliensis	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12608844]
NPO3613	Eriobotrya deflexa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11473413]
NPO40968	0stoc sp. ATCC53789	Strain	0stocaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11170666]
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	aerial part	n.a.	DOI[10.1021/jo00416a020]
NPO834	Peperomia clusiifolia	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5335	0stoc sp	Species	0stocaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO8623	Anneissia japonica	Species	Comatulidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 10 of 35 entries

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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	8

Activity Type	# Activity
Cell Line	2
Individual Protein	3
Others	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT91	Cell Line	KB	Homo sapiens	IC50	=	1000.0	nM	PMID[449471]
NPT114	Cell Line	LoVo	Homo sapiens	IC50	=	1000.0	nM	PMID[449471]
NPT1720	Individual Protein	Plasminogen	Homo sapiens	IC50	<	50000.0	nM	PMID[449471]
NPT201	Individual Protein	Papain	Carica papaya	IC50	<	25000.0	nM	PMID[449471]
NPT2	Others	Unspecified	""	IC50	<	50000.0	nM	PMID[449471]
NPT2	Others	Unspecified	""	IC50	<	25000.0	nM	PMID[449471]
NPT670	Individual Protein	Thrombin	Homo sapiens	IC50	<	50000.0	nM	PMID[449471]

Showing 1 to 7 of 7 entries

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☑ 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 NPC244509 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	170
0.1-0.2	1058
0.2-0.3	6586
0.3-0.4	10797
0.4-0.5	16564
0.5-0.6	6233
0.6-0.7	905
0.7-0.8	313
0.8-0.85	55
0.85-0.9	12
0.9-0.95	2
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.9793	High Similarity	NPC244336
0.931	High Similarity	NPC473491
0.9054	High Similarity	NPC56685
0.894	High Similarity	NPC323336
0.894	High Similarity	NPC326349

Showing 1 to 5 of 200 entries

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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 NPC244509 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	125
0.1-0.2	403
0.2-0.3	761
0.3-0.4	1756
0.4-0.5	3519
0.5-0.6	2081
0.6-0.7	474
0.7-0.8	29
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8693	High Similarity	NPD7118	Clinical (unspecified phase)
0.825	Intermediate Similarity	NPD8303	Discontinued
0.7961	Intermediate Similarity	NPD7978	Discontinued
0.7697	Intermediate Similarity	NPD8172	Phase 2
0.7697	Intermediate Similarity	NPD8173	Phase 2

Showing 1 to 5 of 200 entries

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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