NPASS Compound

Structure

CID287757 OpenBabel06191716092D 48 49 0 0 1 0 0 0 0 0999 V2000 -5.1962 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 7.5000 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 -3.4641 2.0000 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 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 6.0000 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 -6.0622 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 11.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 9.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 4.5000 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 -8.6603 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 3.5000 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 -0.8660 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 -0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 8.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 5.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7942 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 0 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 -0.8660 3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 6.0000 0.0000 C 0 0 1 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 -6.0622 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 5.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 6.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 6.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 7.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 8.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 9 3 0 0 0 0 5 40 1 0 0 0 0 6 41 1 0 0 0 0 7 42 1 0 0 0 0 8 48 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 13 1 0 0 0 0 12 14 2 0 0 0 0 12 15 1 0 0 0 0 13 16 1 0 0 0 0 14 17 1 0 0 0 0 15 18 2 0 0 0 0 16 25 1 0 0 0 0 17 28 2 0 0 0 0 18 28 1 0 0 0 0 19 21 1 0 0 0 0 19 29 2 0 0 0 0 20 22 2 0 0 0 0 20 29 1 0 0 0 0 21 30 2 0 0 0 0 22 30 1 0 0 0 0 23 29 1 0 0 0 0 24 28 1 0 0 0 0 25 2 1 1 0 0 0 25 35 1 0 0 0 0 26 3 1 6 0 0 0 26 36 1 0 0 0 0 26 39 1 0 0 0 0 27 4 1 6 0 0 0 27 37 1 0 0 0 0 27 40 1 0 0 0 0 30 48 1 0 0 0 0 31 23 1 6 0 0 0 31 33 1 0 0 0 0 31 41 1 0 0 0 0 32 24 1 6 0 0 0 32 34 1 0 0 0 0 32 42 1 0 0 0 0 33 38 2 0 0 0 0 33 43 1 0 0 0 0 34 39 2 3 0 0 0 34 44 1 0 0 0 0 35 42 1 0 0 0 0 35 45 2 0 0 0 0 36 40 1 0 0 0 0 36 46 2 0 0 0 0 37 41 1 0 0 0 0 37 47 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	661.38
Volume:	704.846
LogP:	2.699
LogD:	2.451
LogS:	-3.915
# Rotatable Bonds:	22
TPSA:	142.35
# H-Bond Aceptor:	11
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.186
Synthetic Accessibility Score:	4.288
Fsp3:	0.486
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:	-4.947
MDCK Permeability:	5.716405212297104e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.227
20% Bioavailability (F20%):	0.224
30% Bioavailability (F30%):	0.457

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.021
Plasma Protein Binding (PPB):	93.90457916259766%
Volume Distribution (VD):	0.639
Pgp-substrate:	3.180375337600708%

ADMET: Metabolism

CYP1A2-inhibitor:	0.007
CYP1A2-substrate:	0.124
CYP2C19-inhibitor:	0.313
CYP2C19-substrate:	0.808
CYP2C9-inhibitor:	0.646
CYP2C9-substrate:	0.091
CYP2D6-inhibitor:	0.046
CYP2D6-substrate:	0.246
CYP3A4-inhibitor:	0.972
CYP3A4-substrate:	0.909

ADMET: Excretion

Clearance (CL):	5.405
Half-life (T1/2):	0.271

ADMET: Toxicity

hERG Blockers:	0.078
Human Hepatotoxicity (H-HT):	0.934
Drug-inuced Liver Injury (DILI):	0.943
AMES Toxicity:	0.015
Rat Oral Acute Toxicity:	0.576
Maximum Recommended Daily Dose:	0.836
Skin Sensitization:	0.041
Carcinogencity:	0.007
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.031

Download Data

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

Natural Product: NPC287757

Natural Product ID:	NPC287757
*Common Name:**	Dragomabin
IUPAC Name:	(2S)-N-[(2S)-1-[[(2S)-1-[[(2S)-1-[[(2S)-1-amino-3-(4-methoxyphenyl)-1-oxopropan-2-yl]-methylamino]-1-oxopropan-2-yl]-methylamino]-1-oxopropan-2-yl]amino]-1-oxo-3-phenylpropan-2-yl]-N,2-dimethyloct-7-ynamide
Synonyms:	Dragomabin
Standard InCHIKey:	JAYHQHZOWYDLDQ-PONGSQKHSA-N
Standard InCHI:	InChI=1S/C37H51N5O6/c1-9-10-11-13-16-25(2)35(45)42(7)32(24-28-17-14-12-15-18-28)34(44)39-26(3)36(46)40(5)27(4)37(47)41(6)31(33(38)43)23-29-19-21-30(48-8)22-20-29/h1,12,14-15,17-22,25-27,31-32H,10-11,13,16,23-24H2,2-8H3,(H2,38,43)(H,39,44)/t25-,26-,27-,31-,32-/m0/s1
SMILES:	C#CCCCC[C@H](C)C(=O)N(C)[C@@H](Cc1ccccc1)C(=N[C@@H](C)C(=O)N(C)[C@@H](C)C(=O)N(C)[C@@H](Cc1ccc(cc1)OC)C(=N)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL391000
PubChem CID:	16737469
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

*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	2

Activity Type	# Activity
Cell Line	1
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT189	Cell Line	Vero	Chlorocebus aethiops	IC50	=	182300.0	nM	PMID[515825]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	21000.0	nM	PMID[515825]

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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 NPC287757 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	198
0.1-0.2	1225
0.2-0.3	6245
0.3-0.4	10956
0.4-0.5	8408
0.5-0.6	13673
0.6-0.7	1638
0.7-0.8	323
0.8-0.85	26
0.85-0.9	2
0.9-0.95	1
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC319320
0.9122	High Similarity	NPC324081
0.8854	High Similarity	NPC473502
0.8421	Intermediate Similarity	NPC16188
0.8366	Intermediate Similarity	NPC9373

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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 NPC287757 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	141
0.1-0.2	454
0.2-0.3	858
0.3-0.4	1538
0.4-0.5	2754
0.5-0.6	2448
0.6-0.7	891
0.7-0.8	62
0.8-0.85	3
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
0.8627	High Similarity	NPD7131	Phase 3
0.8333	Intermediate Similarity	NPD7485	Phase 3
0.8333	Intermediate Similarity	NPD7484	Phase 3
0.8171	Intermediate Similarity	NPD7608	Discontinued
0.784	Intermediate Similarity	NPD7118	Clinical (unspecified phase)

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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