NPASS Compound

Structure

NPC31313 OpenBabel07101719252D 33 37 0 0 1 0 0 0 0 0999 V2000 -3.0120 1.0645 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3353 1.2436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4789 -3.3610 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8365 -3.0831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6059 0.6939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6358 1.2152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1748 -3.4372 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3044 -2.6282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0781 -0.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5261 -1.6266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0641 0.1648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2121 0.0241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8622 -3.3050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9758 0.9820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3461 -3.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8822 0.1641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0698 -2.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0598 -1.7188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0781 -1.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6794 -1.1768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2121 -2.9759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8610 -0.4516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3461 -0.4759 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4800 -2.9759 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4139 0.5645 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3461 -1.4759 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2291 -0.6614 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2531 -1.3610 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2121 -1.9759 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -0.3665 -0.8190 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 1.0948 -0.8211 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4800 -1.9759 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 2 1 0 0 0 0 1 5 1 0 0 0 0 2 6 1 0 0 0 0 3 4 1 0 0 0 0 3 7 1 0 0 0 0 4 8 1 0 0 0 0 5 11 1 0 0 0 0 6 14 1 0 0 0 0 7 13 1 0 0 0 0 8 17 1 0 0 0 0 9 12 1 0 0 0 0 9 19 1 0 0 0 0 10 18 1 0 0 0 0 10 20 1 0 0 0 0 12 23 1 0 0 0 0 15 21 1 0 0 0 0 15 24 1 0 0 0 0 16 22 1 0 0 0 0 16 25 1 0 0 0 0 17 28 1 0 0 0 0 18 28 1 0 0 0 0 19 29 1 0 0 0 0 20 30 1 0 0 0 0 21 29 1 0 0 0 0 22 30 1 0 0 0 0 23 11 1 1 0 0 0 23 26 1 0 0 0 0 24 13 1 6 0 0 0 24 32 1 0 0 0 0 25 14 1 1 0 0 0 25 33 1 0 0 0 0 26 29 1 6 0 0 0 26 32 1 0 0 0 0 27 28 1 1 0 0 0 27 30 1 0 0 0 0 27 33 1 0 0 0 0 28 31 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	462.38
Volume:	498.426
LogP:	5.832
LogD:	4.231
LogS:	-5.302
# Rotatable Bonds:	0
TPSA:	45.17
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.519
Synthetic Accessibility Score:	5.838
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.943
MDCK Permeability:	1.0904069313255604e-05
Pgp-inhibitor:	0.038
Pgp-substrate:	0.909
Human Intestinal Absorption (HIA):	0.025
20% Bioavailability (F20%):	0.819
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.077
Plasma Protein Binding (PPB):	86.7582778930664%
Volume Distribution (VD):	1.014
Pgp-substrate:	5.275079727172852%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.144
CYP2C19-inhibitor:	0.035
CYP2C19-substrate:	0.915
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.023
CYP2D6-inhibitor:	0.959
CYP2D6-substrate:	0.859
CYP3A4-inhibitor:	0.075
CYP3A4-substrate:	0.234

ADMET: Excretion

Clearance (CL):	4.012
Half-life (T1/2):	0.059

ADMET: Toxicity

hERG Blockers:	0.717
Human Hepatotoxicity (H-HT):	0.79
Drug-inuced Liver Injury (DILI):	0.365
AMES Toxicity:	0.073
Rat Oral Acute Toxicity:	0.025
Maximum Recommended Daily Dose:	0.629
Skin Sensitization:	0.972
Carcinogencity:	0.156
Eye Corrosion:	0.01
Eye Irritation:	0.057
Respiratory Toxicity:	0.892

Download Data

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

Natural Product: NPC31313

Natural Product ID:	NPC31313
*Common Name:**	DAHFKODECRYGAQ-HKVPEBPQSA-N
IUPAC Name:	n.a.
Synonyms:	(+)-Xestospongin D
Standard InCHIKey:	DAHFKODECRYGAQ-HKVPEBPQSA-N
Standard InCHI:	InChI=1S/C28H50N2O3/c31-28-17-8-4-3-7-13-24-15-21-29-19-9-12-23(26(29)32-24)11-5-1-2-6-14-25-16-22-30(20-10-18-28)27(28)33-25/h23-27,31H,1-22H2/t23-,24-,25-,26+,27+,28-/m1/s1
SMILES:	C1CCC[C@@H]2CCN3CCC[C@](CCCCCC[C@@H]4CCN5CCC[C@@H](CC1)[C@@H]5O4)([C@@H]3O2)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL517183
PubChem CID:	10939521
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000195] Piperidines

*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
NPO32702	xestospongia sp.	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11908959]
NPO32702	xestospongia sp.	Species	Petrosiidae	Eukaryota	n.a.	Caledonian	n.a.	PMID[1453184]
NPO32702	xestospongia sp.	Species	Petrosiidae	Eukaryota	n.a.	Thai	n.a.	PMID[14640515]
NPO32702	xestospongia sp.	Species	Petrosiidae	Eukaryota	n.a.	thai	n.a.	PMID[15217287]
NPO32702	xestospongia sp.	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[1710256]
NPO32702	xestospongia sp.	Species	Petrosiidae	Eukaryota	n.a.	coral reef habitat at a depth of approximately 20 m from the sea bed surface, at Sangalaki, Indonesia (2 04 59 N, 118 23 41 E)	1996-MAR	PMID[20503979]
NPO32702	xestospongia sp.	Species	Petrosiidae	Eukaryota	n.a.	Indonesia	n.a.	PMID[20503979]
NPO32702	xestospongia sp.	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[31260310]
NPO32702	xestospongia sp.	Species	Petrosiidae	Eukaryota	n.a.	Philippine	n.a.	PMID[7473578]
NPO32702	xestospongia sp.	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[7798966]

☑ 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
MIC	4

Activity Type	# Activity
Organism	4
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	100.0	ug.mL-1	PMID[506946]
NPT554	Organism	Candida glabrata	Candida glabrata	MIC	=	100.0	ug.mL-1	PMID[506946]
NPT187	Organism	Issatchenkia orientalis	Pichia kudriavzevii	MIC	=	100.0	ug.mL-1	PMID[506946]
NPT2	Others	Unspecified		ED50	=	0.8	uM	PMID[506946]

☑ 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 NPC31313 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	162
0.1-0.2	4658
0.2-0.3	21595
0.3-0.4	11373
0.4-0.5	4503
0.5-0.6	376
0.6-0.7	21
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	1
0.95-1	6

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC288415
1.0	High Similarity	NPC45906
1.0	High Similarity	NPC149908
0.9868	High Similarity	NPC93630
0.9737	High Similarity	NPC81006
0.9221	High Similarity	NPC90839
0.8667	High Similarity	NPC127553
0.8667	High Similarity	NPC255050
0.6795	Remote Similarity	NPC112398
0.6774	Remote Similarity	NPC168017
0.6703	Remote Similarity	NPC124359
0.6632	Remote Similarity	NPC178632
0.618	Remote Similarity	NPC477002
0.6145	Remote Similarity	NPC233034
0.6078	Remote Similarity	NPC313821
0.6022	Remote Similarity	NPC471420
0.593	Remote Similarity	NPC126664
0.593	Remote Similarity	NPC34291
0.5882	Remote Similarity	NPC238646
0.5865	Remote Similarity	NPC91036
0.5859	Remote Similarity	NPC470284
0.5833	Remote Similarity	NPC163134
0.5833	Remote Similarity	NPC471419
0.5825	Remote Similarity	NPC119225
0.5825	Remote Similarity	NPC476261
0.5825	Remote Similarity	NPC471635
0.5825	Remote Similarity	NPC25033
0.5825	Remote Similarity	NPC470382
0.581	Remote Similarity	NPC220111
0.5806	Remote Similarity	NPC150557
0.5794	Remote Similarity	NPC314387
0.5769	Remote Similarity	NPC243635
0.5769	Remote Similarity	NPC151004
0.5769	Remote Similarity	NPC228980
0.5758	Remote Similarity	NPC470282
0.573	Remote Similarity	NPC476696
0.573	Remote Similarity	NPC476695
0.573	Remote Similarity	NPC476694
0.5701	Remote Similarity	NPC144714
0.5701	Remote Similarity	NPC100810
0.5686	Remote Similarity	NPC145707
0.5679	Remote Similarity	NPC293551
0.5673	Remote Similarity	NPC155985
0.5641	Remote Similarity	NPC475887
0.5607	Remote Similarity	NPC56298
0.5607	Remote Similarity	NPC471628
0.56	Remote Similarity	NPC52533

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 NPC31313 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	108
0.1-0.2	1814
0.2-0.3	4860
0.3-0.4	1912
0.4-0.5	327
0.5-0.6	121
0.6-0.7	8
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6168	Remote Similarity	NPD8140	Approved
0.6145	Remote Similarity	NPD9440	Discontinued
0.6087	Remote Similarity	NPD8347	Approved
0.6087	Remote Similarity	NPD8345	Approved
0.6087	Remote Similarity	NPD8346	Approved
0.6078	Remote Similarity	NPD3190	Approved
0.6078	Remote Similarity	NPD3189	Approved
0.6078	Remote Similarity	NPD3191	Approved
0.6019	Remote Similarity	NPD8307	Discontinued
0.593	Remote Similarity	NPD9443	Clinical (unspecified phase)
0.5872	Remote Similarity	NPD7646	Clinical (unspecified phase)
0.5844	Remote Similarity	NPD7348	Clinical (unspecified phase)
0.5794	Remote Similarity	NPD3183	Approved
0.5794	Remote Similarity	NPD3184	Approved
0.5794	Remote Similarity	NPD3182	Approved
0.5794	Remote Similarity	NPD3185	Approved
0.5783	Remote Similarity	NPD9022	Phase 2
0.5783	Remote Similarity	NPD9024	Phase 2
0.5769	Remote Similarity	NPD1821	Approved
0.5769	Remote Similarity	NPD1822	Approved
0.5769	Remote Similarity	NPD1823	Approved
0.573	Remote Similarity	NPD7535	Discontinued
0.5729	Remote Similarity	NPD883	Phase 2
0.5729	Remote Similarity	NPD882	Phase 2
0.5714	Remote Similarity	NPD8087	Discontinued
0.5699	Remote Similarity	NPD8143	Approved
0.5699	Remote Similarity	NPD8144	Approved
0.5696	Remote Similarity	NPD312	Clinical (unspecified phase)
0.5663	Remote Similarity	NPD9455	Approved
0.5618	Remote Similarity	NPD2696	Approved
0.5618	Remote Similarity	NPD2695	Approved
0.5618	Remote Similarity	NPD2697	Approved
0.5618	Remote Similarity	NPD2694	Approved
0.5607	Remote Similarity	NPD4838	Approved
0.5607	Remote Similarity	NPD4836	Approved
0.5607	Remote Similarity	NPD4835	Approved
0.5607	Remote Similarity	NPD4837	Approved
0.5604	Remote Similarity	NPD355	Phase 2

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