NPASS Compound

Structure

CID314854 OpenBabel06191716132D 23 23 0 0 1 0 0 0 0 0999 V2000 5.1962 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 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 3.4641 4.0000 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 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2321 1.8660 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 -2.2321 1.8660 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 4.3301 4.5000 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 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7321 1.0000 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 -1.7321 1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.7321 1.0000 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 0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2321 0.1340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7321 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 12 1 0 0 0 0 2 12 1 0 0 0 0 3 4 1 0 0 0 0 3 5 2 0 0 0 0 4 6 2 0 0 0 0 5 12 1 0 0 0 0 6 16 1 0 0 0 0 7 9 2 0 0 0 0 7 14 1 0 0 0 0 8 10 1 0 0 0 0 8 15 1 0 0 0 0 9 17 1 0 0 0 0 10 17 1 0 0 0 0 11 13 2 0 0 0 0 11 17 1 0 0 0 0 13 14 1 0 0 0 0 13 19 1 0 0 0 0 14 20 2 0 0 0 0 15 18 2 0 0 0 0 15 21 1 0 0 0 0 16 19 2 3 0 0 0 16 22 1 0 0 0 0 17 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	318.16
Volume:	332.731
LogP:	0.357
LogD:	-0.225
LogS:	-1.364
# Rotatable Bonds:	7
TPSA:	109.82
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	1
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.721
Synthetic Accessibility Score:	4.339
Fsp3:	0.412
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.754
MDCK Permeability:	2.3241766029968858e-05
Pgp-inhibitor:	0.501
Pgp-substrate:	0.152
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.999
Plasma Protein Binding (PPB):	69.62602996826172%
Volume Distribution (VD):	0.381
Pgp-substrate:	43.26370620727539%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.139
CYP2C19-inhibitor:	0.027
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.026
CYP2C9-substrate:	0.147
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.105
CYP3A4-inhibitor:	0.018
CYP3A4-substrate:	0.214

ADMET: Excretion

Clearance (CL):	5.112
Half-life (T1/2):	0.498

ADMET: Toxicity

hERG Blockers:	0.03
Human Hepatotoxicity (H-HT):	0.586
Drug-inuced Liver Injury (DILI):	0.06
AMES Toxicity:	0.074
Rat Oral Acute Toxicity:	0.395
Maximum Recommended Daily Dose:	0.943
Skin Sensitization:	0.951
Carcinogencity:	0.906
Eye Corrosion:	0.003
Eye Irritation:	0.019
Respiratory Toxicity:	0.963

Download Data

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

Natural Product: NPC314854

Natural Product ID:	NPC314854
*Common Name:**	Daryamide C
IUPAC Name:	(2E,4E)-N-[3-(3-amino-3-oxopropyl)-3-hydroxy-6-oxocyclohexa-1,4-dien-1-yl]-6-methylhepta-2,4-dienamide
Synonyms:	Daryamide C
Standard InCHIKey:	ZQYBDDWUEWCXIM-GGWOSOGESA-N
Standard InCHI:	InChI=1S/C17H22N2O4/c1-12(2)5-3-4-6-16(22)19-13-11-17(23,9-7-14(13)20)10-8-15(18)21/h3-7,9,11-12,23H,8,10H2,1-2H3,(H2,18,21)(H,19,22)/b5-3+,6-4+
SMILES:	CC(C)C=CC=CC(=O)NC1=CC(C=CC1=O)(CCC(=O)N)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL463898
PubChem CID:	16099483
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000331] Fatty amides [CHEMONTID:0001096] N-acyl amines

*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
NPO32837	streptomyces strain cnq-085	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17190455]

☑ 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
IC50	1

Activity Type	# Activity
Cell Line	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	=	10.03	ug.mL-1	PMID[552584]

☑ 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 NPC314854 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	59
0.1-0.2	646
0.2-0.3	19857
0.3-0.4	17345
0.4-0.5	4304
0.5-0.6	434
0.6-0.7	45
0.7-0.8	5
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC313911
0.7582	Intermediate Similarity	NPC116930
0.75	Intermediate Similarity	NPC472614
0.73	Intermediate Similarity	NPC133729
0.7125	Intermediate Similarity	NPC471022
0.7097	Intermediate Similarity	NPC472613
0.68	Remote Similarity	NPC245650
0.6667	Remote Similarity	NPC170375
0.6598	Remote Similarity	NPC205546
0.6598	Remote Similarity	NPC233273
0.6598	Remote Similarity	NPC189764
0.6598	Remote Similarity	NPC50902
0.6591	Remote Similarity	NPC471597
0.6582	Remote Similarity	NPC77891
0.6538	Remote Similarity	NPC6795
0.6514	Remote Similarity	NPC316325
0.6436	Remote Similarity	NPC313234
0.6375	Remote Similarity	NPC471023
0.6364	Remote Similarity	NPC271621
0.6364	Remote Similarity	NPC59751
0.6364	Remote Similarity	NPC27413
0.6346	Remote Similarity	NPC472615
0.625	Remote Similarity	NPC82674
0.625	Remote Similarity	NPC472616
0.619	Remote Similarity	NPC472433
0.6184	Remote Similarity	NPC184014
0.6184	Remote Similarity	NPC132669
0.6184	Remote Similarity	NPC44193
0.6184	Remote Similarity	NPC246519
0.6184	Remote Similarity	NPC14234
0.6184	Remote Similarity	NPC269800
0.6182	Remote Similarity	NPC471645
0.6173	Remote Similarity	NPC247769
0.6145	Remote Similarity	NPC187315
0.6129	Remote Similarity	NPC471595
0.6126	Remote Similarity	NPC7905
0.6126	Remote Similarity	NPC315652
0.6104	Remote Similarity	NPC471992
0.6092	Remote Similarity	NPC314678
0.6091	Remote Similarity	NPC5485
0.6053	Remote Similarity	NPC473808
0.6053	Remote Similarity	NPC303672
0.6049	Remote Similarity	NPC273614
0.6027	Remote Similarity	NPC91044
0.6026	Remote Similarity	NPC4881
0.6	Remote Similarity	NPC145032
0.6	Remote Similarity	NPC304223
0.6	Remote Similarity	NPC267340
0.6	Remote Similarity	NPC312826
0.6	Remote Similarity	NPC243539
0.6	Remote Similarity	NPC54542
0.6	Remote Similarity	NPC315915
0.5977	Remote Similarity	NPC95863
0.5934	Remote Similarity	NPC55732
0.5921	Remote Similarity	NPC195986
0.5909	Remote Similarity	NPC153660
0.5904	Remote Similarity	NPC253468
0.5904	Remote Similarity	NPC235311
0.5897	Remote Similarity	NPC471991
0.5897	Remote Similarity	NPC297020
0.5897	Remote Similarity	NPC273023
0.5882	Remote Similarity	NPC473249
0.5872	Remote Similarity	NPC175585
0.587	Remote Similarity	NPC157173
0.5867	Remote Similarity	NPC307435
0.5867	Remote Similarity	NPC267692
0.5862	Remote Similarity	NPC203819
0.5844	Remote Similarity	NPC119655
0.5843	Remote Similarity	NPC122244
0.5825	Remote Similarity	NPC265662
0.5823	Remote Similarity	NPC477049
0.5823	Remote Similarity	NPC306420
0.5823	Remote Similarity	NPC24216
0.5823	Remote Similarity	NPC261158
0.5823	Remote Similarity	NPC104138
0.581	Remote Similarity	NPC175531
0.5802	Remote Similarity	NPC150505
0.5802	Remote Similarity	NPC74617
0.5794	Remote Similarity	NPC469958
0.5769	Remote Similarity	NPC56028
0.5769	Remote Similarity	NPC163912
0.5769	Remote Similarity	NPC167759
0.5769	Remote Similarity	NPC305288
0.5769	Remote Similarity	NPC474127
0.5765	Remote Similarity	NPC129995
0.5765	Remote Similarity	NPC315141
0.575	Remote Similarity	NPC268185
0.5739	Remote Similarity	NPC296361
0.573	Remote Similarity	NPC12815
0.573	Remote Similarity	NPC215745
0.573	Remote Similarity	NPC238948
0.5729	Remote Similarity	NPC161670
0.5714	Remote Similarity	NPC263266
0.5698	Remote Similarity	NPC106613
0.5684	Remote Similarity	NPC39966
0.5684	Remote Similarity	NPC224072
0.5682	Remote Similarity	NPC4706
0.5679	Remote Similarity	NPC325734
0.5663	Remote Similarity	NPC269737
0.5663	Remote Similarity	NPC64985
0.5657	Remote Similarity	NPC320057
0.5657	Remote Similarity	NPC316186
0.5647	Remote Similarity	NPC477525
0.5632	Remote Similarity	NPC117804
0.5618	Remote Similarity	NPC316185
0.5607	Remote Similarity	NPC469598
0.5604	Remote Similarity	NPC166018
0.5604	Remote Similarity	NPC169056
0.5604	Remote Similarity	NPC225665

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 NPC314854 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	65
0.1-0.2	318
0.2-0.3	5065
0.3-0.4	3367
0.4-0.5	292
0.5-0.6	35
0.6-0.7	8
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6667	Remote Similarity	NPD7116	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD7601	Clinical (unspecified phase)
0.6514	Remote Similarity	NPD7500	Approved
0.6392	Remote Similarity	NPD2252	Approved
0.6392	Remote Similarity	NPD2251	Approved
0.614	Remote Similarity	NPD7739	Clinical (unspecified phase)
0.6087	Remote Similarity	NPD7624	Clinical (unspecified phase)
0.6087	Remote Similarity	NPD7623	Phase 3
0.5904	Remote Similarity	NPD1984	Approved
0.5882	Remote Similarity	NPD7746	Phase 1
0.5882	Remote Similarity	NPD3709	Clinical (unspecified phase)
0.5882	Remote Similarity	NPD7747	Phase 1
0.5859	Remote Similarity	NPD6094	Approved
0.5859	Remote Similarity	NPD6095	Approved
0.5789	Remote Similarity	NPD7505	Discontinued
0.5769	Remote Similarity	NPD9652	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