NPASS Compound

Structure

NPC244219 OpenBabel06302215082D 48 49 0 0 1 0 0 0 0 0999 V2000 0.6928 -1.3393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2097 -0.9573 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7510 -1.7742 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5508 -2.3405 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.5012 -2.5795 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4409 -3.5576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5637 -3.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7467 -3.4531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1305 -3.8900 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.9475 -3.3486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8247 -3.7855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8871 -2.3705 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7041 -1.8292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5813 -2.2660 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.3983 -1.7247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6437 -0.8510 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4738 -2.4591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7709 -3.3929 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3372 -1.9954 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.9516 -2.7589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9748 -1.2512 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.6722 -2.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5209 -1.7412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3696 -2.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2183 -1.7412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2183 -0.7612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3696 -0.2712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5209 -0.7612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3005 -0.3269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2703 0.6526 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.8884 1.5551 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2061 2.2587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3158 2.6683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3377 2.7286 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.4038 2.4315 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6403 1.8171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1503 0.9684 0.0000 C 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 0.7740 1.2941 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9402 3.2949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0393 3.3251 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4561 4.1281 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5549 3.6187 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7053 2.0964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6450 3.0746 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5825 1.6596 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2689 -0.4772 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0474 -2.4565 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 38 1 0 0 0 0 3 4 2 3 0 0 0 3 48 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 1 0 0 0 5 17 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 3 0 0 0 13 16 1 0 0 0 0 14 15 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 1 0 0 0 21 29 1 0 0 0 0 22 23 1 0 0 0 0 23 28 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 29 30 2 3 0 0 0 29 47 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 31 44 1 6 0 0 0 32 33 1 0 0 0 0 33 34 2 3 0 0 0 33 43 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 35 40 1 6 0 0 0 36 37 1 0 0 0 0 37 38 2 3 0 0 0 37 39 1 0 0 0 0 40 41 2 0 0 0 0 40 42 1 0 0 0 0 44 45 2 0 0 0 0 44 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	675.3
Volume:	648.263
LogP:	-2.867
LogD:	-0.621
LogS:	-1.369
# Rotatable Bonds:	11
TPSA:	291.81
# H-Bond Aceptor:	19
# H-Bond Donor:	10
# Rings:	2
# Heavy Atoms:	19

MedChem Properties

QED Drug-Likeness Score:	0.077
Synthetic Accessibility Score:	5.231
Fsp3:	0.483
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:	-7.75
MDCK Permeability:	2.75107377092354e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.823
20% Bioavailability (F20%):	0.997
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.168
Plasma Protein Binding (PPB):	19.74319839477539%
Volume Distribution (VD):	0.5
Pgp-substrate:	71.60359954833984%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.003
CYP2C19-inhibitor:	0.03
CYP2C19-substrate:	0.025
CYP2C9-inhibitor:	0.213
CYP2C9-substrate:	0.448
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.085
CYP3A4-inhibitor:	0.007
CYP3A4-substrate:	0.0

ADMET: Excretion

Clearance (CL):	1.853
Half-life (T1/2):	0.817

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.129
Drug-inuced Liver Injury (DILI):	0.813
AMES Toxicity:	0.017
Rat Oral Acute Toxicity:	0.039
Maximum Recommended Daily Dose:	0.089
Skin Sensitization:	0.251
Carcinogencity:	0.207
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.909

Download Data

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

Natural Product: NPC244219

Natural Product ID:	NPC244219
*Common Name:**	UHBHXSDKGLPPGO-HTDHLNIYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UHBHXSDKGLPPGO-HTDHLNIYSA-N
Standard InCHI:	InChI=1S/C29H41N9O10/c1-15-23(41)35-17(10-7-11-32-28(30)37-29(48)31-2)25(43)38(3)20(12-16-8-5-4-6-9-16)24(42)36-19(27(46)47)14-22(40)34-18(26(44)45)13-21(39)33-15/h4-6,8-9,15,17-20H,7,10-14H2,1-3H3,(H,33,39)(H,34,40)(H,35,41)(H,36,42)(H,44,45)(H,46,47)(H4,30,31,32,37,48)/t15-,17+,18+,19+,20+/m1/s1
SMILES:	C[C@@H]1C(=N[C@@H](CCCNC(=N)NC(=NC)O)C(=O)N(C)[C@@H](Cc2ccccc2)C(=N[C@@H](CC(=N[C@@H](CC(=N1)O)C(=O)O)O)C(=O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	449124
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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO2567	Serratia marcescens	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	PMID[14325279]
NPO2567	Serratia marcescens	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15853884]
NPO2567	Serratia marcescens	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	PMID[18313305]
NPO2567	Serratia marcescens	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	PMID[783153]
NPO2567	Serratia marcescens	Species	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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	9
Kd	1
Ki	2

Activity Type	# Activity
Individual Protein	8
Others	1
SINGLE PROTEIN	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3501	Individual Protein	Chitinase B	Serratia marcescens	IC50	=	100.0	nM	PMID[18313305]
NPT3501	Individual Protein	Chitinase B	Serratia marcescens	IC50	=	6400.0	nM	PMID[19297173]
NPT3501	Individual Protein	Chitinase B	Serratia marcescens	IC50	=	6400.0	nM	PMID[19395258]
NPT3100	Individual Protein	Acidic mammalian chitinase	Homo sapiens	IC50	=	4500.0	nM	PMID[19666229]
NPT3501	Individual Protein	Chitinase B	Serratia marcescens	IC50	=	6400.0	nM	PMID[20667742]
NPT3501	Individual Protein	Chitinase B	Serratia marcescens	Kd	=	33000.0	nM	PMID[20667742]
NPT3501	Individual Protein	Chitinase B	Serratia marcescens	IC50	=	6400.0	nM	PMID[26030312]
NPT18993	SINGLE PROTEIN	Chitinase	Aspergillus fumigatus	Ki	=	17.0	nM	PMID[16153835]
NPT2	Others	Unspecified		Ki	=	33000.0	nM	PMID[18313305]
NPT18994	SINGLE PROTEIN	Chitinase A	Serratia marcescens	IC50	=	25.0	nM	PMID[19297173]
NPT18995	SINGLE PROTEIN	Chitinase C1	Serratia marcescens	IC50	>	30000.0	nM	PMID[19297173]

☑ 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 NPC244219 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	163
0.1-0.2	1374
0.2-0.3	10409
0.3-0.4	21182
0.4-0.5	7539
0.5-0.6	1366
0.6-0.7	444
0.7-0.8	209
0.8-0.85	8
0.85-0.9	2
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID

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 NPC244219 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	108
0.1-0.2	316
0.2-0.3	899
0.3-0.4	2203
0.4-0.5	3998
0.5-0.6	1363
0.6-0.7	205
0.7-0.8	53
0.8-0.85	3
0.85-0.9	0
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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