NPASS Compound

Structure

CID328457 OpenBabel06191716202D 23 22 0 0 1 0 0 0 0 0999 V2000 -4.3301 0.5000 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 -5.1962 -0.0000 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 -4.3301 1.5000 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 -5.1962 -1.0000 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 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 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 0.8660 0.5000 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 -6.9282 2.0000 0.0000 N 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 0.8660 1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 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 -3.4641 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 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 1 3 1 0 0 0 0 1 5 1 0 0 0 0 2 4 1 0 0 0 0 2 6 1 0 0 0 0 3 7 1 0 0 0 0 5 18 1 0 0 0 0 6 19 1 0 0 0 0 7 9 1 0 0 0 0 7 13 1 1 0 0 0 8 4 1 1 0 0 0 8 10 1 0 0 0 0 8 20 1 0 0 0 0 9 20 2 3 0 0 0 9 21 1 0 0 0 0 10 22 2 0 0 0 0 10 23 1 0 0 0 0 11 14 2 0 0 0 0 11 15 1 0 0 0 0 11 18 1 0 0 0 0 12 16 2 0 0 0 0 12 17 1 0 0 0 0 12 19 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	330.21
Volume:	319.907
LogP:	-3.861
LogD:	-2.404
LogS:	-1.2
# Rotatable Bonds:	13
TPSA:	218.72
# H-Bond Aceptor:	11
# H-Bond Donor:	12
# Rings:	0
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.112
Synthetic Accessibility Score:	3.211
Fsp3:	0.667
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.77
MDCK Permeability:	0.0006046922644600272
Pgp-inhibitor:	0.003
Pgp-substrate:	0.706
Human Intestinal Absorption (HIA):	0.069
20% Bioavailability (F20%):	0.023
30% Bioavailability (F30%):	0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.537
Plasma Protein Binding (PPB):	7.221159934997559%
Volume Distribution (VD):	0.579
Pgp-substrate:	88.81475830078125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.013
CYP2C19-inhibitor:	0.01
CYP2C19-substrate:	0.031
CYP2C9-inhibitor:	0.006
CYP2C9-substrate:	0.005
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.26
CYP3A4-inhibitor:	0.001
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	2.029
Half-life (T1/2):	0.514

ADMET: Toxicity

hERG Blockers:	0.14
Human Hepatotoxicity (H-HT):	0.035
Drug-inuced Liver Injury (DILI):	0.01
AMES Toxicity:	0.023
Rat Oral Acute Toxicity:	0.148
Maximum Recommended Daily Dose:	0.027
Skin Sensitization:	0.18
Carcinogencity:	0.069
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.289

Download Data

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

Natural Product: NPC328457

Natural Product ID:	NPC328457
*Common Name:**	Arg-Arg
IUPAC Name:	(2S)-2-[[(2S)-2-amino-5-(diaminomethylideneamino)pentanoyl]amino]-5-(diaminomethylideneamino)pentanoic acid
Synonyms:	Arg-Arg
Standard InCHIKey:	OMLWNBVRVJYMBQ-YUMQZZPRSA-N
Standard InCHI:	InChI=1S/C12H26N8O3/c13-7(3-1-5-18-11(14)15)9(21)20-8(10(22)23)4-2-6-19-12(16)17/h7-8H,1-6,13H2,(H,20,21)(H,22,23)(H4,14,15,18)(H4,16,17,19)/t7-,8-/m0/s1
SMILES:	C(CC(C(=O)NC(CCCN=C(N)N)C(=O)O)N)CN=C(N)N
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL296756
PubChem CID:	151956
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
NPO30193	Mycoplasma genitalium	Species	Mycoplasmataceae	Bacteria	n.a.	n.a.	n.a.	PMID[22817898]

☑ 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
ED50	1
IC50	1
Ki	1
MIC	3

Activity Type	# Activity
Individual Protein	1
Organism	4
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1237	Individual Protein	Oligopeptide transporter small intestine isoform	Homo sapiens	IC50	=	7310000.0	nM	PMID[502484]
NPT2	Others	Unspecified		Ki	>	100000.0	nM	PMID[502483]
NPT32	Organism	Mus musculus	Mus musculus	ED50	>	50.0	ug mouse-1	PMID[502483]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	1520000.0	nM	PMID[502485]
NPT3145	Organism	Bacillus subtilis subsp. spizizenii ATCC 6633	Bacillus subtilis subsp. spizizenii ATCC 6633	MIC	>	1520000.0	nM	PMID[502485]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	1520000.0	nM	PMID[502485]

☑ 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 NPC328457 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	1780
0.1-0.2	30056
0.2-0.3	8431
0.3-0.4	1631
0.4-0.5	513
0.5-0.6	214
0.6-0.7	56
0.7-0.8	6
0.8-0.85	2
0.85-0.9	5
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8923	High Similarity	NPC103130
0.8923	High Similarity	NPC226453
0.8824	High Similarity	NPC133183
0.8657	High Similarity	NPC327985
0.8333	Intermediate Similarity	NPC118429
0.8235	Intermediate Similarity	NPC278881
0.7662	Intermediate Similarity	NPC191774
0.75	Intermediate Similarity	NPC320598
0.7246	Intermediate Similarity	NPC254541
0.7246	Intermediate Similarity	NPC321536
0.7101	Intermediate Similarity	NPC189301
0.7101	Intermediate Similarity	NPC176164
0.7	Intermediate Similarity	NPC321468
0.7	Intermediate Similarity	NPC316826
0.7	Intermediate Similarity	NPC317143
0.7	Intermediate Similarity	NPC327748
0.6901	Remote Similarity	NPC143722
0.6901	Remote Similarity	NPC329564
0.6901	Remote Similarity	NPC327170
0.6892	Remote Similarity	NPC325534
0.6866	Remote Similarity	NPC245768
0.6812	Remote Similarity	NPC38463
0.6812	Remote Similarity	NPC325985
0.6769	Remote Similarity	NPC93081
0.6769	Remote Similarity	NPC140872
0.6714	Remote Similarity	NPC318260
0.6714	Remote Similarity	NPC317147
0.6714	Remote Similarity	NPC278209
0.662	Remote Similarity	NPC245346
0.662	Remote Similarity	NPC11433
0.662	Remote Similarity	NPC302003
0.6618	Remote Similarity	NPC190184
0.6618	Remote Similarity	NPC197087
0.6533	Remote Similarity	NPC325597
0.6533	Remote Similarity	NPC174304
0.6522	Remote Similarity	NPC321118
0.6522	Remote Similarity	NPC316889
0.6494	Remote Similarity	NPC319046
0.6494	Remote Similarity	NPC81647
0.6471	Remote Similarity	NPC202525
0.6429	Remote Similarity	NPC10915
0.6429	Remote Similarity	NPC322573
0.641	Remote Similarity	NPC126779
0.64	Remote Similarity	NPC289691
0.64	Remote Similarity	NPC315744
0.6375	Remote Similarity	NPC315897
0.6351	Remote Similarity	NPC322206
0.6296	Remote Similarity	NPC320221
0.6212	Remote Similarity	NPC297220
0.6203	Remote Similarity	NPC322274
0.6197	Remote Similarity	NPC327831
0.6176	Remote Similarity	NPC316231
0.6176	Remote Similarity	NPC112890
0.6176	Remote Similarity	NPC324825
0.6133	Remote Similarity	NPC314510
0.6081	Remote Similarity	NPC268927
0.6081	Remote Similarity	NPC64250
0.6081	Remote Similarity	NPC276928
0.6061	Remote Similarity	NPC118459
0.6061	Remote Similarity	NPC327698
0.6056	Remote Similarity	NPC279661
0.6056	Remote Similarity	NPC183845
0.6038	Remote Similarity	NPC259586
0.6029	Remote Similarity	NPC153370
0.6026	Remote Similarity	NPC287693
0.6024	Remote Similarity	NPC327272
0.6	Remote Similarity	NPC322946
0.6	Remote Similarity	NPC472579
0.6	Remote Similarity	NPC276294
0.6	Remote Similarity	NPC321419
0.5981	Remote Similarity	NPC222481
0.5981	Remote Similarity	NPC470621
0.5974	Remote Similarity	NPC57420
0.5949	Remote Similarity	NPC78312
0.5949	Remote Similarity	NPC221764
0.5949	Remote Similarity	NPC135539
0.5949	Remote Similarity	NPC196359
0.5942	Remote Similarity	NPC328378
0.5909	Remote Similarity	NPC53858
0.5909	Remote Similarity	NPC84128
0.5882	Remote Similarity	NPC59867
0.5882	Remote Similarity	NPC315780
0.587	Remote Similarity	NPC304454
0.5844	Remote Similarity	NPC327252
0.5833	Remote Similarity	NPC60672
0.5833	Remote Similarity	NPC322091
0.5802	Remote Similarity	NPC15864
0.5795	Remote Similarity	NPC475542
0.5789	Remote Similarity	NPC177191
0.5783	Remote Similarity	NPC55274
0.5778	Remote Similarity	NPC199072
0.5775	Remote Similarity	NPC19576
0.5775	Remote Similarity	NPC29950
0.5745	Remote Similarity	NPC304455
0.5729	Remote Similarity	NPC216278
0.5714	Remote Similarity	NPC174246
0.5714	Remote Similarity	NPC84636
0.5714	Remote Similarity	NPC62045
0.5714	Remote Similarity	NPC43204
0.5714	Remote Similarity	NPC226027
0.5714	Remote Similarity	NPC162620
0.5714	Remote Similarity	NPC245027
0.5694	Remote Similarity	NPC329495
0.5694	Remote Similarity	NPC189178
0.5694	Remote Similarity	NPC263065
0.5672	Remote Similarity	NPC40511
0.5658	Remote Similarity	NPC476537
0.5658	Remote Similarity	NPC216415
0.5652	Remote Similarity	NPC101249
0.5638	Remote Similarity	NPC320057
0.5634	Remote Similarity	NPC137958
0.5634	Remote Similarity	NPC273330
0.5634	Remote Similarity	NPC319175
0.5634	Remote Similarity	NPC327239
0.5632	Remote Similarity	NPC37681
0.5625	Remote Similarity	NPC470108

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 NPC328457 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	145
0.1-0.2	3811
0.2-0.3	4114
0.3-0.4	736
0.4-0.5	220
0.5-0.6	86
0.6-0.7	24
0.7-0.8	5
0.8-0.85	3
0.85-0.9	4
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9412	High Similarity	NPD366	Approved
0.8923	High Similarity	NPD9045	Approved
0.8923	High Similarity	NPD9046	Phase 3
0.8923	High Similarity	NPD9047	Approved
0.8923	High Similarity	NPD9048	Approved
0.8806	High Similarity	NPD9231	Phase 3
0.8806	High Similarity	NPD9233	Phase 3
0.8806	High Similarity	NPD9232	Phase 2
0.8333	Intermediate Similarity	NPD9014	Approved
0.8077	Intermediate Similarity	NPD4829	Discontinued
0.791	Intermediate Similarity	NPD1155	Discontinued
0.7887	Intermediate Similarity	NPD9451	Clinical (unspecified phase)
0.7662	Intermediate Similarity	NPD4278	Clinical (unspecified phase)
0.7333	Intermediate Similarity	NPD5386	Phase 2
0.6962	Remote Similarity	NPD9224	Clinical (unspecified phase)
0.6892	Remote Similarity	NPD8952	Approved
0.6857	Remote Similarity	NPD9433	Approved
0.6769	Remote Similarity	NPD8809	Approved
0.6769	Remote Similarity	NPD8808	Approved
0.6702	Remote Similarity	NPD6120	Clinical (unspecified phase)
0.662	Remote Similarity	NPD8865	Approved
0.6618	Remote Similarity	NPD8785	Approved
0.6579	Remote Similarity	NPD1429	Clinical (unspecified phase)
0.6533	Remote Similarity	NPD348	Approved
0.6494	Remote Similarity	NPD4241	Registered
0.6494	Remote Similarity	NPD9452	Clinical (unspecified phase)
0.6494	Remote Similarity	NPD337	Discontinued
0.6421	Remote Similarity	NPD4825	Clinical (unspecified phase)
0.641	Remote Similarity	NPD4242	Approved
0.6375	Remote Similarity	NPD6944	Clinical (unspecified phase)
0.6375	Remote Similarity	NPD1825	Clinical (unspecified phase)
0.6364	Remote Similarity	NPD886	Clinical (unspecified phase)
0.6329	Remote Similarity	NPD2702	Phase 1
0.6329	Remote Similarity	NPD2704	Phase 3
0.625	Remote Similarity	NPD5382	Phase 2
0.618	Remote Similarity	NPD7760	Phase 2
0.618	Remote Similarity	NPD7759	Phase 2
0.6176	Remote Similarity	NPD9044	Approved
0.6049	Remote Similarity	NPD2262	Clinical (unspecified phase)
0.6029	Remote Similarity	NPD8614	Approved
0.6022	Remote Similarity	NPD4261	Phase 1
0.6	Remote Similarity	NPD3213	Discontinued
0.6	Remote Similarity	NPD9441	Phase 2
0.598	Remote Similarity	NPD1827	Clinical (unspecified phase)
0.598	Remote Similarity	NPD1828	Approved
0.598	Remote Similarity	NPD1829	Clinical (unspecified phase)
0.5976	Remote Similarity	NPD1147	Phase 2
0.5955	Remote Similarity	NPD3733	Clinical (unspecified phase)
0.5949	Remote Similarity	NPD8868	Approved
0.5942	Remote Similarity	NPD9016	Clinical (unspecified phase)
0.5921	Remote Similarity	NPD574	Approved
0.5909	Remote Similarity	NPD1125	Discovery
0.589	Remote Similarity	NPD8980	Approved
0.589	Remote Similarity	NPD8979	Approved
0.589	Remote Similarity	NPD8981	Clinical (unspecified phase)
0.5851	Remote Similarity	NPD6431	Approved
0.5851	Remote Similarity	NPD6432	Approved
0.5851	Remote Similarity	NPD6434	Clinical (unspecified phase)
0.5851	Remote Similarity	NPD6433	Approved
0.5844	Remote Similarity	NPD575	Clinical (unspecified phase)
0.5842	Remote Similarity	NPD6122	Discontinued
0.5823	Remote Similarity	NPD2703	Discontinued
0.5778	Remote Similarity	NPD326	Approved
0.5775	Remote Similarity	NPD8846	Approved
0.5775	Remote Similarity	NPD61	Approved
0.5775	Remote Similarity	NPD8847	Approved
0.5729	Remote Similarity	NPD6427	Approved
0.5729	Remote Similarity	NPD6426	Approved
0.5729	Remote Similarity	NPD6425	Approved
0.5729	Remote Similarity	NPD6423	Approved
0.5714	Remote Similarity	NPD9017	Approved
0.5714	Remote Similarity	NPD9018	Approved
0.5699	Remote Similarity	NPD3177	Phase 3
0.5694	Remote Similarity	NPD9204	Approved
0.5694	Remote Similarity	NPD9205	Approved
0.5679	Remote Similarity	NPD322	Phase 1
0.5673	Remote Similarity	NPD8175	Discontinued
0.567	Remote Similarity	NPD6424	Approved
0.5657	Remote Similarity	NPD8038	Phase 2
0.5652	Remote Similarity	NPD8867	Approved
0.5652	Remote Similarity	NPD8866	Approved
0.5647	Remote Similarity	NPD9367	Discontinued
0.5634	Remote Similarity	NPD8871	Approved
0.5634	Remote Similarity	NPD8872	Phase 3

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