NPASS Compound

Structure

NPC51702 OpenBabel06302215532D 29 33 0 0 0 0 0 0 0 0999 V2000 6.8339 -3.6774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1648 -2.9343 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1867 -3.1422 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8776 -4.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5468 -4.8364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5249 -4.6285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0468 -5.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4535 -6.6160 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0686 -5.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -1.5000 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -0.5000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 5.6962 -1.5000 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -4.5000 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -6.5000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 2.2321 -7.5000 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 10 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 10 1 0 0 0 0 10 19 1 0 0 0 0 10 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 29 1 0 0 0 0 14 15 2 0 0 0 0 14 28 1 0 0 0 0 15 16 1 0 0 0 0 15 27 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 26 1 0 0 0 0 22 23 1 0 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 M CHG 2 25 -1 28 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	835.66
Volume:	430.388
LogP:	5.935
LogD:	2.423
LogS:	-3.117
# Rotatable Bonds:	0
TPSA:	75.99
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.212
Synthetic Accessibility Score:	3.803
Fsp3:	0.05
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.175
MDCK Permeability:	1.712675111775752e-05
Pgp-inhibitor:	0.026
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.135
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	100.05400848388672%
Volume Distribution (VD):	0.398
Pgp-substrate:	2.111661434173584%

ADMET: Metabolism

CYP1A2-inhibitor:	0.12
CYP1A2-substrate:	0.498
CYP2C19-inhibitor:	0.244
CYP2C19-substrate:	0.122
CYP2C9-inhibitor:	0.879
CYP2C9-substrate:	0.448
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.145
CYP3A4-inhibitor:	0.138
CYP3A4-substrate:	0.499

ADMET: Excretion

Clearance (CL):	2.238
Half-life (T1/2):	0.764

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.064
Drug-inuced Liver Injury (DILI):	0.372
AMES Toxicity:	0.035
Rat Oral Acute Toxicity:	0.934
Maximum Recommended Daily Dose:	0.992
Skin Sensitization:	0.948
Carcinogencity:	0.04
Eye Corrosion:	0.003
Eye Irritation:	0.913
Respiratory Toxicity:	0.557

Download Data

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

Natural Product: NPC51702

Natural Product ID:	NPC51702
*Common Name:**	RAGZEDHHTPQLAI-UHFFFAOYSA-L
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RAGZEDHHTPQLAI-UHFFFAOYSA-L
Standard InCHI:	InChI=1S/C20H8I4O5.2Na/c21-11-5-9-17(13(23)15(11)25)28-18-10(6-12(22)16(26)14(18)24)20(9)8-4-2-1-3-7(8)19(27)29-20;;/h1-6,25-26H;;/q;2*+1/p-2
SMILES:	c1ccc2c(c1)C(=O)OC12c2cc(c(c(c2Oc2c1cc(c(c2I)[O-])I)I)[O-])I.[Na+].[Na+]
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	12961638
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes

*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
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1002/hlca.19270100148]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	Petals	n.a.	n.a.	PMID[15043425]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24338885]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	Silk Stigma Style	n.a.	n.a.	Database[FooDB]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9445	Crocus sativus	Species	Iridaceae	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	6
Others	2

Activity Type	# Activity
Others	1
PROTEIN COMPLEX	10
SINGLE PROTEIN	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT21773	SINGLE PROTEIN	Thiosulfate sulfurtransferase	Homo sapiens	IC50	=	9200.0	nM	PMID[533186]
NPT2	Others	Unspecified		IC50	=	33000.0	nM	PMID[533186]
NPT21772	PROTEIN COMPLEX	GroEL/GroES	Escherichia coli	IC50	=	1200.0	nM	PMID[533186]
NPT21772	PROTEIN COMPLEX	GroEL/GroES	Escherichia coli	IC50	=	500.0	nM	PMID[533186]
NPT21774	PROTEIN COMPLEX	HSP60/HSP10	Homo sapiens	IC50	=	2900.0	nM	PMID[533186]
NPT21775	SINGLE PROTEIN	60 kDa chaperonin	Escherichia coli (strain K12)	IC50	=	222000.0	nM	PMID[533186]
NPT21772	PROTEIN COMPLEX	GroEL/GroES	Escherichia coli	Inhibition	=	82.0	%	PMID[533186]
NPT21772	PROTEIN COMPLEX	GroEL/GroES	Escherichia coli	Inhibition	=	84.0	%	PMID[533186]

☑ 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 NPC51702 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	514
0.1-0.2	2071
0.2-0.3	4834
0.3-0.4	11983
0.4-0.5	5795
0.5-0.6	4994
0.6-0.7	7997
0.7-0.8	4492
0.8-0.85	15
0.85-0.9	0
0.9-0.95	0
0.95-1	2

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 NPC51702 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	444
0.1-0.2	1018
0.2-0.3	1533
0.3-0.4	2819
0.4-0.5	1856
0.5-0.6	1035
0.6-0.7	329
0.7-0.8	111
0.8-0.85	4
0.85-0.9	0
0.9-0.95	1
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