NPASS Compound

Structure

NPC107836 OpenBabel07101718192D 36 42 0 0 1 0 0 0 0 0999 V2000 3.9905 2.4659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3704 3.2395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9905 1.4659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5783 2.2614 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1245 2.9659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4193 3.5485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1245 0.9659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8352 1.5922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0181 -1.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2584 2.4659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6762 2.8794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2584 1.4659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8841 1.9013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1045 -0.9945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3074 2.7749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6817 2.9839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9006 3.6884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0939 3.7930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7196 1.9659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2749 2.0704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7045 -1.5823 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6180 -1.1756 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7226 -0.1810 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3074 4.6020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3018 4.7711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9135 0.4067 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3074 1.1568 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.5642 5.2711 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.0181 1.4013 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.1226 -2.3958 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6000 -2.5768 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4271 -1.7634 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6361 0.2257 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2855 4.8099 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2153 5.1778 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 3 2 0 0 0 0 1 5 1 0 0 0 0 2 4 2 0 0 0 0 2 6 1 0 0 0 0 3 7 1 0 0 0 0 4 8 1 0 0 0 0 5 10 2 0 0 0 0 6 11 2 0 0 0 0 7 12 2 0 0 0 0 8 13 2 0 0 0 0 9 30 1 0 0 0 0 10 12 1 0 0 0 0 10 15 1 0 0 0 0 11 13 1 0 0 0 0 11 16 1 0 0 0 0 12 27 1 0 0 0 0 13 29 1 0 0 0 0 14 9 1 6 0 0 0 14 21 1 0 0 0 0 14 36 1 0 0 0 0 15 17 2 0 0 0 0 15 19 1 0 0 0 0 16 18 2 0 0 0 0 16 20 1 0 0 0 0 17 18 1 0 0 0 0 17 24 1 0 0 0 0 18 25 1 0 0 0 0 19 20 2 0 0 0 0 19 27 1 0 0 0 0 20 29 1 0 0 0 0 21 22 1 0 0 0 0 21 31 1 1 0 0 0 22 23 1 0 0 0 0 22 32 1 6 0 0 0 23 26 1 0 0 0 0 23 33 1 1 0 0 0 24 28 2 0 0 0 0 24 34 1 0 0 0 0 25 28 1 0 0 0 0 25 35 2 0 0 0 0 26 29 1 6 0 0 0 26 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	487.14
Volume:	463.878
LogP:	0.887
LogD:	2.158
LogS:	-5.236
# Rotatable Bonds:	2
TPSA:	157.04
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	7
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.205
Synthetic Accessibility Score:	4.014
Fsp3:	0.231
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.864
MDCK Permeability:	5.023980065743672e-06
Pgp-inhibitor:	0.123
Pgp-substrate:	0.292
Human Intestinal Absorption (HIA):	0.968
20% Bioavailability (F20%):	0.897
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.13
Plasma Protein Binding (PPB):	91.29236602783203%
Volume Distribution (VD):	0.802
Pgp-substrate:	2.832751750946045%

ADMET: Metabolism

CYP1A2-inhibitor:	0.753
CYP1A2-substrate:	0.053
CYP2C19-inhibitor:	0.103
CYP2C19-substrate:	0.068
CYP2C9-inhibitor:	0.489
CYP2C9-substrate:	0.235
CYP2D6-inhibitor:	0.499
CYP2D6-substrate:	0.126
CYP3A4-inhibitor:	0.208
CYP3A4-substrate:	0.049

ADMET: Excretion

Clearance (CL):	2.719
Half-life (T1/2):	0.377

ADMET: Toxicity

hERG Blockers:	0.061
Human Hepatotoxicity (H-HT):	0.285
Drug-inuced Liver Injury (DILI):	0.969
AMES Toxicity:	0.369
Rat Oral Acute Toxicity:	0.007
Maximum Recommended Daily Dose:	0.506
Skin Sensitization:	0.58
Carcinogencity:	0.891
Eye Corrosion:	0.003
Eye Irritation:	0.031
Respiratory Toxicity:	0.591

Download Data

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

Natural Product: NPC107836

Natural Product ID:	NPC107836
*Common Name:**	FAKJOUAYZNXZGV-QCUUGYDUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FAKJOUAYZNXZGV-QCUUGYDUSA-N
Standard InCHI:	InChI=1S/C26H21N3O7/c30-9-14-21(31)22(32)23(33)26(36-14)29-13-8-4-2-6-11(13)16-18-17(24(34)28-25(18)35)15-10-5-1-3-7-12(10)27-19(15)20(16)29/h1-8,14,21-23,26-27,30-33H,9H2,(H,28,34,35)/t14-,21-,22+,23-,26-/m1/s1
SMILES:	OC[C@H]1O[C@H]([C@@H]([C@H]([C@@H]1O)O)O)n1c2c(c3c1cccc3)c1C(=O)N=C(c1c1c2[nH]c2c1cccc2)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3589062
PubChem CID:	465911
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000211] Indoles and derivatives [CHEMONTID:0000210] Carbazoles [CHEMONTID:0001865] Pyrrolocarbazoles [CHEMONTID:0001866] Indolocarbazoles

*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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO33195	actinomadura melliaura atcc 39691	Species	Thermomonosporaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26091285]

Showing 1 to 1 of 1 entries

Previous1Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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
Others	3

Activity Type	# Activity
Cell Line	2
NON-MOLECULAR	1

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	Activity	=	32.6	%	PMID[507684]
NPT306	Cell Line	PC-3	Homo sapiens	Activity	=	47.7	%	PMID[507684]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	53.6	%	PMID[507684]

Showing 1 to 3 of 3 entries

Previous1Next

☑ 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 NPC107836 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	444
0.1-0.2	2083
0.2-0.3	10166
0.3-0.4	16097
0.4-0.5	9180
0.5-0.6	2694
0.6-0.7	1864
0.7-0.8	146
0.8-0.85	15
0.85-0.9	5
0.9-0.95	2
0.95-1	1

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
0.9142	High Similarity	NPC1203
0.9107	High Similarity	NPC472207
0.875	High Similarity	NPC472842
0.871	High Similarity	NPC31700
0.8571	High Similarity	NPC472843

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC107836 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	230
0.1-0.2	604
0.2-0.3	847
0.3-0.4	1958
0.4-0.5	2822
0.5-0.6	2010
0.6-0.7	623
0.7-0.8	46
0.8-0.85	5
0.85-0.9	4
0.9-0.95	1
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9103	High Similarity	NPD6456	Discontinued
0.8735	High Similarity	NPD7181	Phase 3
0.8701	High Similarity	NPD7921	Approved
0.8496	Intermediate Similarity	NPD6978	Phase 2
0.8496	Intermediate Similarity	NPD6977	Clinical (unspecified phase)

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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