NPASS Compound

Structure

NPC306696 OpenBabel07101718282D 35 34 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 -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 -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 -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 -4.3301 -3.5000 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 -4.5000 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 -2.5981 -1.5000 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 -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 -3.4641 -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 -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 -11.2583 -7.5000 0.0000 C 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 -8.6603 -6.0000 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 -2.5981 -3.5000 0.0000 O 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 -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 -8.0000 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 -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 18 1 0 0 0 0 2 18 1 0 0 0 0 3 5 1 0 0 0 0 3 7 1 0 0 0 0 4 6 1 0 0 0 0 4 8 1 0 0 0 0 5 14 1 0 0 0 0 6 13 1 0 0 0 0 7 15 1 0 0 0 0 8 16 1 0 0 0 0 9 11 1 0 0 0 0 9 19 1 0 0 0 0 10 12 1 0 0 0 0 10 20 1 0 0 0 0 11 21 1 0 0 0 0 12 23 1 0 0 0 0 13 24 1 0 0 0 0 14 25 1 0 0 0 0 15 26 1 0 0 0 0 16 27 1 0 0 0 0 17 18 1 0 0 0 0 17 22 1 0 0 0 0 19 24 2 3 0 0 0 19 28 1 0 0 0 0 20 25 2 3 0 0 0 20 29 1 0 0 0 0 21 26 1 0 0 0 0 21 30 2 0 0 0 0 22 27 1 0 0 0 0 22 31 2 0 0 0 0 23 32 2 0 0 0 0 23 33 1 0 0 0 0 26 34 1 0 0 0 0 27 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	502.3
Volume:	507.491
LogP:	-0.814
LogD:	-0.869
LogS:	-0.957
# Rotatable Bonds:	24
TPSA:	176.58
# H-Bond Aceptor:	12
# H-Bond Donor:	5
# Rings:	0
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.095
Synthetic Accessibility Score:	2.819
Fsp3:	0.783
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:	-5.654
MDCK Permeability:	3.8834536098875105e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.927
Human Intestinal Absorption (HIA):	0.994
20% Bioavailability (F20%):	0.964
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.051
Plasma Protein Binding (PPB):	22.09445571899414%
Volume Distribution (VD):	0.826
Pgp-substrate:	67.44233703613281%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.038
CYP2C19-inhibitor:	0.029
CYP2C19-substrate:	0.035
CYP2C9-inhibitor:	0.055
CYP2C9-substrate:	0.992
CYP2D6-inhibitor:	0.125
CYP2D6-substrate:	0.059
CYP3A4-inhibitor:	0.021
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	9.451
Half-life (T1/2):	0.249

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.27
Drug-inuced Liver Injury (DILI):	0.019
AMES Toxicity:	0.017
Rat Oral Acute Toxicity:	0.067
Maximum Recommended Daily Dose:	0.035
Skin Sensitization:	0.139
Carcinogencity:	0.003
Eye Corrosion:	0.003
Eye Irritation:	0.039
Respiratory Toxicity:	0.002

Download Data

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

Natural Product: NPC306696

Natural Product ID:	NPC306696
*Common Name:**	Tenacibactin C
IUPAC Name:	4-[5-[hydroxy-[4-[5-[hydroxy(3-methylbutanoyl)amino]pentylamino]-4-oxobutanoyl]amino]pentylamino]-4-oxobutanoic acid
Synonyms:	tenacibactin C
Standard InCHIKey:	JNJGHWCLIHDZDM-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C23H42N4O8/c1-18(2)17-22(31)27(35)16-8-4-6-13-24-19(28)9-11-21(30)26(34)15-7-3-5-14-25-20(29)10-12-23(32)33/h18,34-35H,3-17H2,1-2H3,(H,24,28)(H,25,29)(H,32,33)
SMILES:	OC(=NCCCCCN(C(=O)CC(C)C)O)CCC(=O)N(CCCCCN=C(CCC(=O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL224373
PubChem CID:	16216279
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000262] Fatty acids and conjugates [CHEMONTID:0000338] Branched fatty acids

*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	=	110.0	uM	PMID[554480]

☑ 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 NPC306696 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	272
0.1-0.2	21518
0.2-0.3	17655
0.3-0.4	2495
0.4-0.5	496
0.5-0.6	236
0.6-0.7	16
0.7-0.8	0
0.8-0.85	2
0.85-0.9	4
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9194	High Similarity	NPC105297
0.8906	High Similarity	NPC128559
0.8871	High Similarity	NPC263207
0.8788	High Similarity	NPC250953
0.871	High Similarity	NPC292299
0.871	High Similarity	NPC34838
0.8333	Intermediate Similarity	NPC262615
0.7125	Intermediate Similarity	NPC84128
0.7125	Intermediate Similarity	NPC53858
0.6515	Remote Similarity	NPC471131
0.6341	Remote Similarity	NPC31756
0.631	Remote Similarity	NPC246005
0.6277	Remote Similarity	NPC475440
0.6265	Remote Similarity	NPC476156
0.6265	Remote Similarity	NPC476117
0.6265	Remote Similarity	NPC476243
0.6265	Remote Similarity	NPC476137
0.619	Remote Similarity	NPC476302
0.6118	Remote Similarity	NPC184473
0.6118	Remote Similarity	NPC6902
0.6111	Remote Similarity	NPC475801
0.6111	Remote Similarity	NPC474593
0.6104	Remote Similarity	NPC470110
0.6081	Remote Similarity	NPC327252
0.6076	Remote Similarity	NPC196007
0.6076	Remote Similarity	NPC214532
0.6076	Remote Similarity	NPC76297
0.6044	Remote Similarity	NPC474576
0.6044	Remote Similarity	NPC477538
0.6	Remote Similarity	NPC23984
0.5978	Remote Similarity	NPC471098
0.5978	Remote Similarity	NPC62263
0.5978	Remote Similarity	NPC173763
0.5977	Remote Similarity	NPC472351
0.5974	Remote Similarity	NPC470109
0.597	Remote Similarity	NPC80350
0.5949	Remote Similarity	NPC478256
0.593	Remote Similarity	NPC284456
0.5926	Remote Similarity	NPC266888
0.5926	Remote Similarity	NPC256312
0.5926	Remote Similarity	NPC209156
0.5926	Remote Similarity	NPC161774
0.5904	Remote Similarity	NPC59867
0.5895	Remote Similarity	NPC473597
0.589	Remote Similarity	NPC327748
0.589	Remote Similarity	NPC321468
0.589	Remote Similarity	NPC317143
0.589	Remote Similarity	NPC316826
0.5862	Remote Similarity	NPC235078
0.5857	Remote Similarity	NPC316889
0.5857	Remote Similarity	NPC321118
0.5844	Remote Similarity	NPC470108
0.5843	Remote Similarity	NPC477539
0.5833	Remote Similarity	NPC317147
0.5833	Remote Similarity	NPC318260
0.5833	Remote Similarity	NPC316242
0.5823	Remote Similarity	NPC193280
0.5823	Remote Similarity	NPC314273
0.5823	Remote Similarity	NPC472579
0.5814	Remote Similarity	NPC314466
0.5814	Remote Similarity	NPC475542
0.5811	Remote Similarity	NPC329564
0.5811	Remote Similarity	NPC327170
0.5802	Remote Similarity	NPC141325
0.5797	Remote Similarity	NPC322946
0.5795	Remote Similarity	NPC145748
0.5795	Remote Similarity	NPC95478
0.5795	Remote Similarity	NPC155670
0.5789	Remote Similarity	NPC57420
0.5773	Remote Similarity	NPC220234
0.5765	Remote Similarity	NPC478017
0.5765	Remote Similarity	NPC312315
0.5765	Remote Similarity	NPC315535
0.5765	Remote Similarity	NPC315131
0.5743	Remote Similarity	NPC475637
0.5732	Remote Similarity	NPC138435
0.573	Remote Similarity	NPC227051
0.5714	Remote Similarity	NPC473495
0.5696	Remote Similarity	NPC10716
0.5692	Remote Similarity	NPC43264
0.5676	Remote Similarity	NPC321536
0.5632	Remote Similarity	NPC470783
0.5625	Remote Similarity	NPC29598
0.5625	Remote Similarity	NPC126779
0.5625	Remote Similarity	NPC212866
0.5612	Remote Similarity	NPC475758
0.56	Remote Similarity	NPC124554
0.56	Remote Similarity	NPC5864
0.56	Remote Similarity	NPC301148

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 NPC306696 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	74
0.1-0.2	3959
0.2-0.3	4015
0.3-0.4	803
0.4-0.5	219
0.5-0.6	69
0.6-0.7	9
0.7-0.8	1
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8333	Intermediate Similarity	NPD6438	Approved
0.8333	Intermediate Similarity	NPD6437	Approved
0.6786	Remote Similarity	NPD7760	Phase 2
0.6786	Remote Similarity	NPD7759	Phase 2
0.6585	Remote Similarity	NPD612	Discontinued
0.6341	Remote Similarity	NPD4815	Discontinued
0.6333	Remote Similarity	NPD6699	Clinical (unspecified phase)
0.6234	Remote Similarity	NPD3724	Clinical (unspecified phase)
0.6207	Remote Similarity	NPD3723	Clinical (unspecified phase)
0.619	Remote Similarity	NPD7762	Phase 2
0.619	Remote Similarity	NPD7763	Phase 2
0.6184	Remote Similarity	NPD2263	Discontinued
0.617	Remote Similarity	NPD8038	Phase 2
0.6164	Remote Similarity	NPD574	Approved
0.6163	Remote Similarity	NPD3733	Clinical (unspecified phase)
0.6094	Remote Similarity	NPD9658	Clinical (unspecified phase)
0.6081	Remote Similarity	NPD575	Clinical (unspecified phase)
0.6047	Remote Similarity	NPD4829	Discontinued
0.6044	Remote Similarity	NPD4261	Phase 1
0.6026	Remote Similarity	NPD620	Approved
0.5974	Remote Similarity	NPD1429	Clinical (unspecified phase)
0.593	Remote Similarity	NPD2683	Discontinued
0.593	Remote Similarity	NPD1125	Discovery
0.5876	Remote Similarity	NPD6120	Clinical (unspecified phase)
0.5862	Remote Similarity	NPD7643	Phase 1
0.5802	Remote Similarity	NPD6944	Clinical (unspecified phase)
0.5797	Remote Similarity	NPD9441	Phase 2
0.5778	Remote Similarity	NPD3176	Clinical (unspecified phase)
0.5765	Remote Similarity	NPD7917	Clinical (unspecified phase)
0.5765	Remote Similarity	NPD7918	Clinical (unspecified phase)
0.57	Remote Similarity	NPD6122	Discontinued
0.5696	Remote Similarity	NPD322	Phase 1
0.5667	Remote Similarity	NPD5791	Phase 2
0.5632	Remote Similarity	NPD3628	Phase 3
0.5625	Remote Similarity	NPD7841	Clinical (unspecified phase)
0.5625	Remote Similarity	NPD7840	Approved
0.5625	Remote Similarity	NPD4242	Approved
0.5616	Remote Similarity	NPD9425	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