NPASS Compound

Structure

NPC476259 OpenBabel07101719182D 69 69 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 -6.0622 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -9.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 2.5000 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 0.8660 -6.5000 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 -2.5981 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1340 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3660 -2.6340 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 -3.4641 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -9.0000 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 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 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 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 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 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -7.5000 0.0000 C 0 0 1 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 -6.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -8.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 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 -7.7942 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7942 -3.5000 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 -0.8660 -6.5000 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 -6.0622 1.5000 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 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 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 -2.5981 -1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -5.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -7.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -4.5000 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 -0.0000 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -7.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -9.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 16 1 0 0 0 0 2 17 1 0 0 0 0 3 18 1 0 0 0 0 4 27 1 0 0 0 0 5 27 1 0 0 0 0 11 49 1 0 0 0 0 12 49 1 0 0 0 0 13 55 1 0 0 0 0 14 56 1 0 0 0 0 15 57 1 0 0 0 0 16 28 1 0 0 0 0 17 29 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 20 22 1 0 0 0 0 21 23 2 0 0 0 0 22 33 2 0 0 0 0 23 33 1 0 0 0 0 24 33 1 0 0 0 0 25 36 1 0 0 0 0 25 50 1 0 0 0 0 26 37 1 0 0 0 0 26 51 1 0 0 0 0 28 6 1 6 0 0 0 28 39 1 0 0 0 0 29 7 1 1 0 0 0 29 40 1 0 0 0 0 30 8 1 6 0 0 0 30 34 1 0 0 0 0 30 47 1 0 0 0 0 31 9 1 1 0 0 0 31 41 1 0 0 0 0 31 52 1 0 0 0 0 32 10 1 6 0 0 0 32 42 1 0 0 0 0 32 53 1 0 0 0 0 34 18 1 1 0 0 0 34 54 1 0 0 0 0 35 24 1 1 0 0 0 35 43 1 0 0 0 0 35 55 1 0 0 0 0 36 56 1 0 0 0 0 36 58 2 0 0 0 0 37 57 1 0 0 0 0 37 59 2 0 0 0 0 38 27 1 1 0 0 0 38 46 1 0 0 0 0 38 56 1 0 0 0 0 39 44 1 1 0 0 0 39 57 1 0 0 0 0 40 45 1 0 0 0 0 40 60 1 6 0 0 0 41 49 1 0 0 0 0 41 61 2 0 0 0 0 42 54 2 3 0 0 0 42 62 1 0 0 0 0 43 52 2 3 0 0 0 43 63 1 0 0 0 0 44 50 2 3 0 0 0 44 64 1 0 0 0 0 45 51 2 3 0 0 0 45 65 1 0 0 0 0 46 55 1 0 0 0 0 46 66 2 0 0 0 0 47 67 2 0 0 0 0 47 68 1 0 0 0 0 48 49 1 0 0 0 0 48 53 2 3 0 0 0 48 69 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	972.59
Volume:	1006.686
LogP:	2.022
LogD:	1.552
LogS:	-2.583
# Rotatable Bonds:	35
TPSA:	284.52
# H-Bond Aceptor:	20
# H-Bond Donor:	7
# Rings:	1
# Heavy Atoms:	20

MedChem Properties

QED Drug-Likeness Score:	0.036
Synthetic Accessibility Score:	5.838
Fsp3:	0.673
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:	-6.601
MDCK Permeability:	1.1170063771714922e-05
Pgp-inhibitor:	0.703
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.902
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.866

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.079
Plasma Protein Binding (PPB):	59.13958740234375%
Volume Distribution (VD):	0.493
Pgp-substrate:	46.57640075683594%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.009
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.03
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.037
CYP3A4-inhibitor:	0.05
CYP3A4-substrate:	0.046

ADMET: Excretion

Clearance (CL):	4.139
Half-life (T1/2):	0.279

ADMET: Toxicity

hERG Blockers:	0.001
Human Hepatotoxicity (H-HT):	0.971
Drug-inuced Liver Injury (DILI):	0.955
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.02
Maximum Recommended Daily Dose:	0.007
Skin Sensitization:	0.191
Carcinogencity:	0.009
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.815

Download Data

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

Natural Product: NPC476259

Natural Product ID:	NPC476259
*Common Name:**	(2S,3R)-3-[(2S)-2-[(4S)-4-[(2S)-2-[(2S)-2-{2-[(2S,3S)-2-{2-[(2S,3S)-2-Hydroxy-3-Methylpentanamido]-N-Methylacetamido}-3-Methylpentanamido]-N-Methylacetamido}-N,3-Dimethylbutanamido]-3-Phenylpropanamido]-2,2-Dimethyl-3-Oxopentanamido]Propanamido]-2-Methylpentanoic Acid
IUPAC Name:	(2S,3R)-3-[[(2S)-2-[[(4S)-4-[[(2S)-2-[[(2S)-2-[[2-[[(2S,3S)-2-[[2-[[(2S,3S)-2-hydroxy-3-methylpentanoyl]amino]acetyl]-methylamino]-3-methylpentanoyl]amino]acetyl]-methylamino]-3-methylbutanoyl]-methylamino]-3-phenylpropanoyl]amino]-2,2-dimethyl-3-oxopentanoyl]amino]propanoyl]amino]-2-methylpentanoic acid
Synonyms:
Standard InCHIKey:	RHNKFTFBLMRTMD-XPQZGKFDSA-N
Standard InCHI:	InChI=1S/C49H80N8O12/c1-16-28(6)39(57(15)37(59)26-51-45(65)40(60)29(7)17-2)44(64)50-25-36(58)56(14)38(27(4)5)46(66)55(13)35(24-33-22-20-19-21-23-33)43(63)52-31(9)41(61)49(11,12)48(69)53-32(10)42(62)54-34(18-3)30(8)47(67)68/h19-23,27-32,34-35,38-40,60H,16-18,24-26H2,1-15H3,(H,50,64)(H,51,65)(H,52,63)(H,53,69)(H,54,62)(H,67,68)/t28-,29-,30-,31-,32-,34+,35-,38-,39-,40-/m0/s1
SMILES:	CCC(C)C(C(=O)NCC(=O)N(C)C(C(C)C)C(=O)N(C)C(CC1=CC=CC=C1)C(=O)NC(C)C(=O)C(C)(C)C(=O)NC(C)C(=O)NC(CC)C(C)C(=O)O)N(C)C(=O)CNC(=O)C(C(C)CC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL558942
PubChem CID:	44179713
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0002010] Hybrid peptides

*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
NPO26389	Lyngbya majuscula	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9784156]
NPO26389	Lyngbya majuscula	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9599279]
NPO26389	Lyngbya majuscula	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9599278]
NPO26389	Lyngbya majuscula	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9584405]
NPO26389	Lyngbya majuscula	Species	Oscillatoriaceae	Bacteria	n.a.	Caribbean	n.a.	PMID[8699186]
NPO26389	Lyngbya majuscula	Species	Oscillatoriaceae	Bacteria	n.a.	Caribbean	n.a.	PMID[7623050]
NPO26389	Lyngbya majuscula	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[3924698]
NPO26389	Lyngbya majuscula	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[29792428]
NPO26389	Lyngbya majuscula	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[22035372]
NPO26389	Lyngbya majuscula	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21999614]

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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	4
Others	3

Activity Type	# Activity
Cell Line	5
NON-MOLECULAR	1
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	=	16.0	nM	PMID[450703]
NPT397	Cell Line	NCI-H460	Homo sapiens	IC50	=	94.0	nM	PMID[450703]
NPT400	Cell Line	MDA-MB-435	Homo sapiens	IC50	=	230.0	nM	PMID[450703]
NPT393	Cell Line	HCT-116	Homo sapiens	Ratio IC50	=	5.0	n.a.	PMID[450703]
NPT400	Cell Line	MDA-MB-435	Homo sapiens	Ratio IC50	=	5.0	n.a.	PMID[450703]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	1000.0	nM	PMID[450703]
NPT2	Others	Unspecified	""	Ratio IC50	=	10.0	n.a.	PMID[450703]

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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 NPC476259 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	126
0.1-0.2	647
0.2-0.3	3230
0.3-0.4	20267
0.4-0.5	15290
0.5-0.6	2271
0.6-0.7	528
0.7-0.8	280
0.8-0.85	52
0.85-0.9	2
0.9-0.95	2
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.9697	High Similarity	NPC176226
0.9328	High Similarity	NPC168113
0.9259	High Similarity	NPC197682
0.8931	High Similarity	NPC319766
0.8561	High Similarity	NPC268841

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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 NPC476259 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	98
0.1-0.2	319
0.2-0.3	715
0.3-0.4	2600
0.4-0.5	3764
0.5-0.6	1313
0.6-0.7	317
0.7-0.8	24
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8273	Intermediate Similarity	NPD8416	Discontinued
0.8156	Intermediate Similarity	NPD8172	Phase 2
0.8156	Intermediate Similarity	NPD8173	Phase 2
0.7836	Intermediate Similarity	NPD2218	Phase 2
0.7836	Intermediate Similarity	NPD2217	Approved

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