NPASS Compound

Structure

CID98424 OpenBabel06191715442D 48 50 0 0 1 0 0 0 0 0999 V2000 -2.0670 -2.4265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3792 -2.2397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4447 6.5688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4504 7.9371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0943 -2.0414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7898 -1.9478 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5586 -0.8057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1867 -1.2202 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6724 1.9387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8233 2.4289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6724 0.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2796 5.0806 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9743 1.9387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8233 0.4681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2850 4.1003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6019 4.3407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0921 3.4917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3456 5.3785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4927 0.1030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1325 6.3820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1252 0.4681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2770 -1.8459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3425 6.9626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9151 -1.5052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9743 0.9583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2762 0.9583 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3543 3.7922 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7027 0.6836 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0246 5.4075 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1374 4.9846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8611 -0.5263 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1454 1.5584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6470 2.8565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6529 0.2015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9680 5.1408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8866 -0.4184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2801 2.5295 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.6200 1.8765 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.8177 -0.3119 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.7737 4.5821 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.3760 5.8198 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0811 1.2657 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6181 2.9911 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2968 -0.5378 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3864 6.0274 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6199 -1.3618 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0457 5.3535 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 22 1 0 0 0 0 2 22 1 0 0 0 0 3 23 1 0 0 0 0 4 23 1 0 0 0 0 5 24 1 0 0 0 0 6 24 1 0 0 0 0 7 39 1 0 0 0 0 8 40 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 10 13 1 0 0 0 0 11 14 2 0 0 0 0 12 15 1 0 0 0 0 12 18 1 0 0 0 0 13 25 2 0 0 0 0 14 25 1 0 0 0 0 16 17 1 0 0 0 0 16 30 1 0 0 0 0 17 37 1 0 0 0 0 18 41 1 0 0 0 0 19 22 1 0 0 0 0 20 23 1 0 0 0 0 21 25 1 0 0 0 0 26 21 1 1 0 0 0 26 34 1 0 0 0 0 26 38 1 0 0 0 0 27 15 1 1 0 0 0 27 33 1 0 0 0 0 27 41 1 0 0 0 0 28 19 1 1 0 0 0 28 32 1 0 0 0 0 28 39 1 0 0 0 0 29 20 1 1 0 0 0 29 35 1 0 0 0 0 29 48 1 0 0 0 0 30 42 2 0 0 0 0 30 48 1 0 0 0 0 31 24 1 1 0 0 0 31 36 1 0 0 0 0 31 40 1 0 0 0 0 32 37 2 3 0 0 0 32 43 1 0 0 0 0 33 38 2 3 0 0 0 33 44 1 0 0 0 0 34 40 1 0 0 0 0 34 45 2 0 0 0 0 35 41 1 0 0 0 0 35 46 2 0 0 0 0 36 39 1 0 0 0 0 36 47 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	669.41
Volume:	698.33
LogP:	3.619
LogD:	3.762
LogS:	-4.568
# Rotatable Bonds:	7
TPSA:	145.43
# H-Bond Aceptor:	12
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.425
Synthetic Accessibility Score:	4.932
Fsp3:	0.667
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.05
MDCK Permeability:	7.84355797804892e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.559
Human Intestinal Absorption (HIA):	0.02
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.4

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.04
Plasma Protein Binding (PPB):	84.70050048828125%
Volume Distribution (VD):	0.472
Pgp-substrate:	7.329158306121826%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.043
CYP2C19-inhibitor:	0.271
CYP2C19-substrate:	0.657
CYP2C9-inhibitor:	0.57
CYP2C9-substrate:	0.679
CYP2D6-inhibitor:	0.018
CYP2D6-substrate:	0.12
CYP3A4-inhibitor:	0.939
CYP3A4-substrate:	0.817

ADMET: Excretion

Clearance (CL):	8.824
Half-life (T1/2):	0.548

ADMET: Toxicity

hERG Blockers:	0.008
Human Hepatotoxicity (H-HT):	0.96
Drug-inuced Liver Injury (DILI):	0.952
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.94
Maximum Recommended Daily Dose:	0.357
Skin Sensitization:	0.063
Carcinogencity:	0.032
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.008

Download Data

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

Natural Product: NPC98424

Natural Product ID:	NPC98424
*Common Name:**	Pseudodestruxin B
IUPAC Name:	(3S,10S,13S,16S,19S)-16-benzyl-11,14-dimethyl-3,10-bis(2-methylpropyl)-13-propan-2-yl-4-oxa-1,8,11,14,17-pentazabicyclo[17.3.0]docosane-2,5,9,12,15,18-hexone
Synonyms:
Standard InCHIKey:	CNPDLOWQKDIMOD-OLAIZJASSA-N
Standard InCHI:	InChI=1S/C36H55N5O7/c1-22(2)19-28-32(43)37-17-16-30(42)48-29(20-23(3)4)35(46)41-18-12-15-27(41)33(44)38-26(21-25-13-10-9-11-14-25)34(45)40(8)31(24(5)6)36(47)39(28)7/h9-11,13-14,22-24,26-29,31H,12,15-21H2,1-8H3,(H,37,43)(H,38,44)/t26-,27-,28-,29-,31-/m0/s1
SMILES:	CC(C[C@@H]1OC(=O)CCN=C(O)[C@H](CC(C)C)N(C)C(=O)[C@@H](N(C(=O)[C@@H](N=C([C@H]2N(C1=O)CCC2)O)Cc1ccccc1)C)C(C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL447934
PubChem CID:	9986956
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0001961] Depsipeptides [CHEMONTID:0001994] Cyclic depsipeptides

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO17983	Nigrosabulum globosum	Species	Bionectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11374942]
NPO17983	Nigrosabulum globosum	Species	Bionectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13654	Grindelia chiloensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11710	Actinoplanes philippinensis	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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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

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☑ 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	1

Activity Type	# Activity
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	IZ	=	8.0	mm	PMID[506191]

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☑ 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 NPC98424 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	125
0.1-0.2	672
0.2-0.3	3663
0.3-0.4	20989
0.4-0.5	13746
0.5-0.6	2582
0.6-0.7	551
0.7-0.8	254
0.8-0.85	70
0.85-0.9	30
0.9-0.95	5
0.95-1	10

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC470884
1.0	High Similarity	NPC178662
1.0	High Similarity	NPC92784
1.0	High Similarity	NPC476133
0.9624	High Similarity	NPC209509

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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 NPC98424 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	99
0.1-0.2	308
0.2-0.3	641
0.3-0.4	2335
0.4-0.5	3825
0.5-0.6	1516
0.6-0.7	330
0.7-0.8	90
0.8-0.85	2
0.85-0.9	4
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8837	High Similarity	NPD2584	Suspended
0.875	High Similarity	NPD8173	Phase 2
0.875	High Similarity	NPD8172	Phase 2
0.8676	High Similarity	NPD7113	Clinical (unspecified phase)
0.8162	Intermediate Similarity	NPD5339	Clinical (unspecified phase)

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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