NPASS Compound

Structure

CID318700 OpenBabel06191716142D 40 40 0 0 1 0 0 0 0 0999 V2000 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0981 1.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -0.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3660 -1.6340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3660 -3.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -0.6340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8301 -2.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 -3.6340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -5.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4641 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4641 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 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 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4641 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -4.5000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -4.0000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 1 27 1 6 0 0 0 2 4 1 0 0 0 0 2 28 1 1 0 0 0 3 5 1 0 0 0 0 3 29 1 6 0 0 0 4 6 1 0 0 0 0 4 30 1 6 0 0 0 5 6 1 0 0 0 0 5 31 1 6 0 0 0 6 32 1 1 0 0 0 7 34 1 0 0 0 0 8 34 1 0 0 0 0 9 34 2 0 0 0 0 10 35 1 0 0 0 0 11 35 1 0 0 0 0 12 35 2 0 0 0 0 13 36 1 0 0 0 0 14 36 1 0 0 0 0 15 36 2 0 0 0 0 16 37 1 0 0 0 0 17 37 1 0 0 0 0 18 37 2 0 0 0 0 19 38 1 0 0 0 0 20 38 1 0 0 0 0 21 38 2 0 0 0 0 22 39 1 0 0 0 0 23 39 1 0 0 0 0 24 39 2 0 0 0 0 25 40 1 0 0 0 0 26 40 2 0 0 0 0 27 34 1 0 0 0 0 28 35 1 0 0 0 0 29 36 1 0 0 0 0 30 37 1 0 0 0 0 31 38 1 0 0 0 0 32 40 1 0 0 0 0 33 39 1 0 0 0 0 33 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	739.83
Volume:	479.903
LogP:	-4.524
LogD:	-2.209
LogS:	0.509
# Rotatable Bonds:	14
TPSA:	424.97
# H-Bond Aceptor:	27
# H-Bond Donor:	6
# Rings:	1
# Heavy Atoms:	34

MedChem Properties

QED Drug-Likeness Score:	0.107
Synthetic Accessibility Score:	7.916
Fsp3:	1.0
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-7.314
MDCK Permeability:	0.00017345821834169328
Pgp-inhibitor:	0.0
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	1.0
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.191
Plasma Protein Binding (PPB):	10.189210891723633%
Volume Distribution (VD):	0.218
Pgp-substrate:	44.12169647216797%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.034
CYP2C19-substrate:	0.006
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.117
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.016
CYP3A4-inhibitor:	0.0
CYP3A4-substrate:	0.0

ADMET: Excretion

Clearance (CL):	0.313
Half-life (T1/2):	0.513

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.005
Drug-inuced Liver Injury (DILI):	0.0
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.978
Skin Sensitization:	0.589
Carcinogencity:	0.026
Eye Corrosion:	0.993
Eye Irritation:	0.922
Respiratory Toxicity:	0.088

Download Data

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

Natural Product: NPC318700

Natural Product ID:	NPC318700
*Common Name:**	UPHPWXPNZIOZJL-XCMZKKERSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UPHPWXPNZIOZJL-XCMZKKERSA-N
Standard InCHI:	InChI=1S/C6H19O27P7/c7-34(8,9)27-1-2(28-35(10,11)12)4(30-37(16,17)18)6(32-40(25,26)33-39(22,23)24)5(31-38(19,20)21)3(1)29-36(13,14)15/h1-6H,(H,25,26)(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-/m1/s1
SMILES:	OP(=O)(O[C@@H]1[C@@H](OP(=O)(OP(=O)(O)O)O)[C@H](OP(=O)(O)O)[C@@H]([C@@H]([C@H]1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1242023
PubChem CID:	NA
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000129] Alcohols and polyols [CHEMONTID:0001292] Cyclic alcohols and derivatives [CHEMONTID:0002509] Cyclitols and derivatives [CHEMONTID:0002511] Inositol phosphates

*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
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/0003-9861(62)90112-1]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11035032]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12902239]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[13835567]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14389294]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1449509]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14607989]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15375647]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15744050]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16850348]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17439666]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22031445]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2405251]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24305546]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24678285]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24733517]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24831709]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24981409]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2687322]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3289762]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[4266242]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[4616942]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[5764336]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6306574]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[767332]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7929110]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8017107]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8798704]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8852895]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8971708]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9748245]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO21658	Saccharomyces cerevisiae	Species	Saccharomycetaceae	Eukaryota	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	5
Kd	1
Ki	1
Others	1

Activity Type	# Activity
Individual Protein	4
Protein Complex	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6029	Individual Protein	Phosphate system positive regulatory protein PHO81	Saccharomyces cerevisiae S288c	IC50	=	22000.0	nM	PMID[490739]
NPT6029	Individual Protein	Phosphate system positive regulatory protein PHO81	Saccharomyces cerevisiae S288c	IC50	=	31000.0	nM	PMID[490739]
NPT6029	Individual Protein	Phosphate system positive regulatory protein PHO81	Saccharomyces cerevisiae S288c	IC50	=	14000.0	nM	PMID[490739]
NPT6029	Individual Protein	Phosphate system positive regulatory protein PHO81	Saccharomyces cerevisiae S288c	IC50	=	23000.0	nM	PMID[490739]
NPT6028	Protein Complex	Pho80/Pho85/Pho81 complex	Saccharomyces cerevisiae S288c	Kd	=	20300.0	nM	PMID[490739]
NPT6028	Protein Complex	Pho80/Pho85/Pho81 complex	Saccharomyces cerevisiae S288c	Ki	=	19000.0	nM	PMID[490739]
NPT6028	Protein Complex	Pho80/Pho85/Pho81 complex	Saccharomyces cerevisiae S288c	IC50	=	25000.0	nM	PMID[490739]
NPT6030	Protein Complex	Pho80/Pho85	Saccharomyces cerevisiae S288c	FC	=	5.0	n.a.	PMID[490739]

☑ 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 NPC318700 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	2015
0.1-0.2	21119
0.2-0.3	17415
0.3-0.4	1868
0.4-0.5	197
0.5-0.6	57
0.6-0.7	10
0.7-0.8	8
0.8-0.85	0
0.85-0.9	2
0.9-0.95	4
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC188428
0.9167	High Similarity	NPC321102
0.9167	High Similarity	NPC325153
0.9167	High Similarity	NPC322803
0.9167	High Similarity	NPC278465
0.8542	High Similarity	NPC61270
0.8542	High Similarity	NPC325822
0.7755	Intermediate Similarity	NPC314613
0.7069	Intermediate Similarity	NPC174485
0.6875	Remote Similarity	NPC102981
0.6875	Remote Similarity	NPC99573
0.6875	Remote Similarity	NPC227707
0.6875	Remote Similarity	NPC88278
0.6875	Remote Similarity	NPC111882
0.6429	Remote Similarity	NPC320043
0.6429	Remote Similarity	NPC103672
0.6346	Remote Similarity	NPC107091
0.6346	Remote Similarity	NPC207656
0.6316	Remote Similarity	NPC317626
0.6316	Remote Similarity	NPC317501
0.6316	Remote Similarity	NPC314821
0.625	Remote Similarity	NPC329095
0.6111	Remote Similarity	NPC88638
0.6029	Remote Similarity	NPC321873
0.6	Remote Similarity	NPC3547
0.5833	Remote Similarity	NPC66052
0.5833	Remote Similarity	NPC86412
0.5833	Remote Similarity	NPC293908
0.5833	Remote Similarity	NPC325034
0.5833	Remote Similarity	NPC192065

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 NPC318700 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	2356
0.1-0.2	5531
0.2-0.3	954
0.3-0.4	200
0.4-0.5	72
0.5-0.6	28
0.6-0.7	4
0.7-0.8	2
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD9065	Phase 3
0.8958	High Similarity	NPD8991	Phase 1
0.8542	High Similarity	NPD9061	Clinical (unspecified phase)
0.6875	Remote Similarity	NPD8996	Phase 3
0.6875	Remote Similarity	NPD8995	Clinical (unspecified phase)
0.6429	Remote Similarity	NPD9049	Discontinued
0.6429	Remote Similarity	NPD9050	Approved
0.6346	Remote Similarity	NPD9219	Approved
0.6346	Remote Similarity	NPD9218	Clinical (unspecified phase)
0.6316	Remote Similarity	NPD9036	Phase 3
0.6316	Remote Similarity	NPD9035	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD9052	Approved
0.5833	Remote Similarity	NPD9053	Approved
0.5833	Remote Similarity	NPD9051	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