NPASS Compound

Structure

NPC250953 OpenBabel07101718312D 42 41 0 0 0 0 0 0 0 0999 V2000 -2.5981 -2.5000 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 13.8564 9.0000 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 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 9.5000 0.0000 C 0 0 0 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 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 3.0000 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 10.3923 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 6.5000 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 14.7224 10.5000 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 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 7.5000 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 0.8660 -1.5000 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 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 6.5000 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 11.2583 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 5.0000 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 15.5885 11.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 6.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 8.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 4.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 7.5000 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 10.3923 8.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 9.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 23 1 0 0 0 0 2 23 1 0 0 0 0 3 6 1 0 0 0 0 3 9 1 0 0 0 0 4 7 1 0 0 0 0 4 10 1 0 0 0 0 5 8 1 0 0 0 0 5 11 1 0 0 0 0 6 16 1 0 0 0 0 7 17 1 0 0 0 0 8 18 1 0 0 0 0 9 19 1 0 0 0 0 10 20 1 0 0 0 0 11 21 1 0 0 0 0 12 14 1 0 0 0 0 12 24 1 0 0 0 0 13 15 1 0 0 0 0 13 25 1 0 0 0 0 14 26 1 0 0 0 0 15 27 1 0 0 0 0 16 29 1 0 0 0 0 17 30 1 0 0 0 0 18 31 1 0 0 0 0 19 32 1 0 0 0 0 20 33 1 0 0 0 0 21 34 1 0 0 0 0 22 23 1 0 0 0 0 22 28 1 0 0 0 0 24 30 2 3 0 0 0 24 35 1 0 0 0 0 25 31 2 3 0 0 0 25 36 1 0 0 0 0 26 32 1 0 0 0 0 26 37 2 0 0 0 0 27 33 1 0 0 0 0 27 38 2 0 0 0 0 28 34 1 0 0 0 0 28 39 2 0 0 0 0 32 40 1 0 0 0 0 33 41 1 0 0 0 0 34 42 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	602.4
Volume:	615.964
LogP:	0.399
LogD:	-1.438
LogS:	-0.684
# Rotatable Bonds:	30
TPSA:	205.84
# H-Bond Aceptor:	14
# H-Bond Donor:	7
# Rings:	0
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.051
Synthetic Accessibility Score:	3.145
Fsp3:	0.821
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.754
MDCK Permeability:	3.194834789610468e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.981
Human Intestinal Absorption (HIA):	0.998
20% Bioavailability (F20%):	0.996
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.024
Plasma Protein Binding (PPB):	12.373207092285156%
Volume Distribution (VD):	1.348
Pgp-substrate:	71.9536361694336%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.071
CYP2C19-inhibitor:	0.032
CYP2C19-substrate:	0.034
CYP2C9-inhibitor:	0.111
CYP2C9-substrate:	0.978
CYP2D6-inhibitor:	0.024
CYP2D6-substrate:	0.047
CYP3A4-inhibitor:	0.107
CYP3A4-substrate:	0.006

ADMET: Excretion

Clearance (CL):	9.522
Half-life (T1/2):	0.088

ADMET: Toxicity

hERG Blockers:	0.139
Human Hepatotoxicity (H-HT):	0.424
Drug-inuced Liver Injury (DILI):	0.037
AMES Toxicity:	0.021
Rat Oral Acute Toxicity:	0.403
Maximum Recommended Daily Dose:	0.171
Skin Sensitization:	0.338
Carcinogencity:	0.006
Eye Corrosion:	0.003
Eye Irritation:	0.028
Respiratory Toxicity:	0.003

Download Data

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

Natural Product: NPC250953

Natural Product ID:	NPC250953
*Common Name:**	Tenacibactin D
IUPAC Name:	N'-(5-aminopentyl)-N'-hydroxy-N-[5-[hydroxy-[4-[5-[hydroxy(3-methylbutanoyl)amino]pentylamino]-4-oxobutanoyl]amino]pentyl]butanediamide
Synonyms:	tenacibactin D
Standard InCHIKey:	PEWTWABSZJRYMI-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C28H54N6O8/c1-23(2)22-28(39)34(42)21-11-5-8-18-31-25(36)13-15-27(38)33(41)20-10-4-7-17-30-24(35)12-14-26(37)32(40)19-9-3-6-16-29/h23,40-42H,3-22,29H2,1-2H3,(H,30,35)(H,31,36)
SMILES:	CC(C)CC(=O)N(CCCCCN=C(CCC(=O)N(CCCCCN=C(CCC(=O)N(CCCCCN)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL225448
PubChem CID:	16216156
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
NPO32917	tenacibaculum sp. a4k-17	Species	Flavobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17319723]

☑ 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

Activity Type	# Activity
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		ED50	=	115.0	uM	PMID[458388]

☑ 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 NPC250953 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	307
0.1-0.2	25870
0.2-0.3	13837
0.3-0.4	1974
0.4-0.5	493
0.5-0.6	182
0.6-0.7	25
0.7-0.8	1
0.8-0.85	2
0.85-0.9	3
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9516	High Similarity	NPC262615
0.8788	High Similarity	NPC306696
0.871	High Similarity	NPC34838
0.871	High Similarity	NPC292299
0.8571	High Similarity	NPC263207
0.803	Intermediate Similarity	NPC105297
0.7794	Intermediate Similarity	NPC128559
0.6914	Remote Similarity	NPC84128
0.6914	Remote Similarity	NPC53858
0.6515	Remote Similarity	NPC471131
0.6386	Remote Similarity	NPC23984
0.6353	Remote Similarity	NPC472351
0.6341	Remote Similarity	NPC31756
0.6265	Remote Similarity	NPC476243
0.6265	Remote Similarity	NPC476137
0.6265	Remote Similarity	NPC476156
0.6265	Remote Similarity	NPC476117
0.6235	Remote Similarity	NPC235078
0.622	Remote Similarity	NPC191774
0.619	Remote Similarity	NPC476302
0.6164	Remote Similarity	NPC314510
0.6118	Remote Similarity	NPC184473
0.6118	Remote Similarity	NPC6902
0.6111	Remote Similarity	NPC327748
0.6111	Remote Similarity	NPC316826
0.6111	Remote Similarity	NPC317143
0.6111	Remote Similarity	NPC321468
0.6087	Remote Similarity	NPC316889
0.6087	Remote Similarity	NPC301010
0.6087	Remote Similarity	NPC321118
0.6076	Remote Similarity	NPC196007
0.6076	Remote Similarity	NPC76297
0.6076	Remote Similarity	NPC214532
0.6027	Remote Similarity	NPC329564
0.6027	Remote Similarity	NPC327170
0.6026	Remote Similarity	NPC472579
0.6022	Remote Similarity	NPC280066
0.6	Remote Similarity	NPC275715
0.597	Remote Similarity	NPC80350
0.596	Remote Similarity	NPC128303
0.593	Remote Similarity	NPC284456
0.5926	Remote Similarity	NPC266888
0.5926	Remote Similarity	NPC256312
0.5926	Remote Similarity	NPC161774
0.5926	Remote Similarity	NPC209156
0.59	Remote Similarity	NPC241394
0.589	Remote Similarity	NPC216415
0.589	Remote Similarity	NPC321536
0.589	Remote Similarity	NPC476537
0.5843	Remote Similarity	NPC477539
0.5833	Remote Similarity	NPC318260
0.5833	Remote Similarity	NPC317147
0.5823	Remote Similarity	NPC126779
0.5814	Remote Similarity	NPC314466
0.5765	Remote Similarity	NPC312315
0.5747	Remote Similarity	NPC246005
0.5714	Remote Similarity	NPC473495
0.5696	Remote Similarity	NPC470110
0.5676	Remote Similarity	NPC320598
0.5676	Remote Similarity	NPC254541
0.5663	Remote Similarity	NPC327272
0.5625	Remote Similarity	NPC319114
0.5612	Remote Similarity	NPC475440
0.561	Remote Similarity	NPC315897
0.56	Remote Similarity	NPC143722

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 NPC250953 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	84
0.1-0.2	3790
0.2-0.3	4225
0.3-0.4	781
0.4-0.5	198
0.5-0.6	62
0.6-0.7	8
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9516	High Similarity	NPD6438	Approved
0.9516	High Similarity	NPD6437	Approved
0.6786	Remote Similarity	NPD7760	Phase 2
0.6786	Remote Similarity	NPD7759	Phase 2
0.6447	Remote Similarity	NPD620	Approved
0.6341	Remote Similarity	NPD4815	Discontinued
0.6333	Remote Similarity	NPD6699	Clinical (unspecified phase)
0.631	Remote Similarity	NPD2683	Discontinued
0.6304	Remote Similarity	NPD7841	Clinical (unspecified phase)
0.622	Remote Similarity	NPD4278	Clinical (unspecified phase)
0.619	Remote Similarity	NPD7762	Phase 2
0.619	Remote Similarity	NPD7763	Phase 2
0.617	Remote Similarity	NPD8038	Phase 2
0.6163	Remote Similarity	NPD3733	Clinical (unspecified phase)
0.6056	Remote Similarity	NPD9425	Approved
0.6047	Remote Similarity	NPD4829	Discontinued
0.6044	Remote Similarity	NPD5792	Clinical (unspecified phase)
0.6044	Remote Similarity	NPD4261	Phase 1
0.6023	Remote Similarity	NPD3723	Clinical (unspecified phase)
0.6	Remote Similarity	NPD6944	Clinical (unspecified phase)
0.6	Remote Similarity	NPD612	Discontinued
0.5974	Remote Similarity	NPD1429	Clinical (unspecified phase)
0.5972	Remote Similarity	NPD8784	Clinical (unspecified phase)
0.5955	Remote Similarity	NPD3176	Clinical (unspecified phase)
0.593	Remote Similarity	NPD1125	Discovery
0.5876	Remote Similarity	NPD6120	Clinical (unspecified phase)
0.5862	Remote Similarity	NPD7643	Phase 1
0.5823	Remote Similarity	NPD4242	Approved
0.5753	Remote Similarity	NPD9433	Approved
0.5714	Remote Similarity	NPD3177	Phase 3
0.5696	Remote Similarity	NPD322	Phase 1
0.5696	Remote Similarity	NPD4241	Registered
0.5676	Remote Similarity	NPD9670	Phase 2
0.5676	Remote Similarity	NPD9671	Phase 2
0.5667	Remote Similarity	NPD5791	Phase 2
0.5612	Remote Similarity	NPD4825	Clinical (unspecified phase)
0.561	Remote Similarity	NPD266	Phase 3
0.561	Remote Similarity	NPD265	Phase 3
0.561	Remote Similarity	NPD1825	Clinical (unspecified phase)

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