NPASS Compound

Structure

CID58001 OpenBabel06191715392D 38 40 0 0 1 0 0 0 0 0999 V2000 0.3520 -2.4496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9663 -1.3262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6420 2.8949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0889 -2.1930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4784 0.7406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1078 2.5195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7041 1.7148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5961 1.6603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4646 -1.5767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4644 -1.5995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9982 -0.1366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4489 3.2717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3452 3.6634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0261 5.1419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1309 5.7197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2794 4.1201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0172 -1.5073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6586 2.7138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5081 -1.2851 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.7873 4.4933 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1182 5.5611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4215 4.6155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6209 1.8816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4332 -1.3517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1374 5.6062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6657 -0.7462 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1737 3.8118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4397 0.8981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2992 -0.8517 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.2113 5.2287 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.5299 2.8774 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.5335 5.1590 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4099 6.5176 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8106 -2.2777 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0509 4.2920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3894 0.5848 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1374 4.6155 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 17 1 0 0 0 0 2 17 1 0 0 0 0 3 18 1 0 0 0 0 5 7 2 0 0 0 0 5 11 1 0 0 0 0 6 8 1 0 0 0 0 6 12 1 0 0 0 0 7 18 1 0 0 0 0 8 23 2 0 0 0 0 9 10 2 0 0 0 0 9 19 1 0 0 0 0 10 24 1 0 0 0 0 11 29 1 0 0 0 0 12 31 1 0 0 0 0 13 18 2 0 0 0 0 13 20 1 0 0 0 0 14 20 1 0 0 0 0 14 21 1 0 0 0 0 15 21 1 0 0 0 0 15 25 1 0 0 0 0 16 22 2 0 0 0 0 16 37 1 0 0 0 0 19 4 1 1 0 0 0 19 26 1 0 0 0 0 20 32 1 6 0 0 0 21 33 2 0 0 0 0 22 27 1 0 0 0 0 22 30 1 0 0 0 0 23 28 1 0 0 0 0 23 31 1 0 0 0 0 24 29 2 3 0 0 0 24 34 1 0 0 0 0 25 30 2 0 0 0 0 25 37 1 0 0 0 0 26 17 1 1 0 0 0 26 38 1 0 0 0 0 27 31 1 0 0 0 0 27 35 2 0 0 0 0 28 36 2 0 0 0 0 28 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	525.25
Volume:	535.332
LogP:	1.636
LogD:	1.577
LogS:	-3.151
# Rotatable Bonds:	1
TPSA:	139.04
# H-Bond Aceptor:	10
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.421
Synthetic Accessibility Score:	6.13
Fsp3:	0.464
Lipinski Rule-of-5:	Accepted
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:	-4.852
MDCK Permeability:	5.712226538889809e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.974
Human Intestinal Absorption (HIA):	0.016
20% Bioavailability (F20%):	0.212
30% Bioavailability (F30%):	0.526

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.31
Plasma Protein Binding (PPB):	70.9967269897461%
Volume Distribution (VD):	0.596
Pgp-substrate:	35.74839401245117%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.081
CYP2C19-inhibitor:	0.078
CYP2C19-substrate:	0.058
CYP2C9-inhibitor:	0.165
CYP2C9-substrate:	0.14
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.149
CYP3A4-inhibitor:	0.421
CYP3A4-substrate:	0.229

ADMET: Excretion

Clearance (CL):	7.217
Half-life (T1/2):	0.787

ADMET: Toxicity

hERG Blockers:	0.038
Human Hepatotoxicity (H-HT):	0.8
Drug-inuced Liver Injury (DILI):	0.97
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.488
Maximum Recommended Daily Dose:	0.915
Skin Sensitization:	0.222
Carcinogencity:	0.895
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.917

Download Data

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

Natural Product: NPC58001

Natural Product ID:	NPC58001
*Common Name:**	Virginiamycin Factor M1
IUPAC Name:	n.a.
Synonyms:	Virginiamycin Factor M1; Virginiamycin M1
Standard InCHIKey:	DAIKHDNSXMZDCU-FQTGFAPKSA-N
Standard InCHI:	InChI=1S/C28H35N3O7/c1-17(2)26-19(4)9-10-24(34)29-11-5-7-18(3)13-20(32)14-21(33)15-25-30-22(16-37-25)27(35)31-12-6-8-23(31)28(36)38-26/h5,7-10,13,16-17,19-20,26,32H,6,11-12,14-15H2,1-4H3,(H,29,34)/b7-5+,10-9+,18-13+/t19-,20-,26-/m1/s1
SMILES:	CC(C)[C@@H]1[C@H](C)/C=C/C(=NC/C=C/C(=C/[C@H](CC(=O)Cc2nc(co2)C(=O)N2CCC=C2C(=O)O1)O)/C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1236670
PubChem CID:	5459319
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0001900] Macrolide lactams

*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
NPO30193	Mycoplasma genitalium	Species	Mycoplasmataceae	Bacteria	n.a.	n.a.	n.a.	PMID[22817898]
NPO8948	Streptomyces pristinaespiralis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25708513]
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7663	Carex pendula	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7663	Carex pendula	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10141	Alstonia lenormandii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7227	Nepeta tuberosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2225	Neonauclea sessilifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO184	Halobates hayanus	Species	Gerridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8948	Streptomyces pristinaespiralis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO3157	Polysyncraton echinatum	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9874	Gueriniella serratulae	Species	Monophlebidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3349	Cryptosporiopsis abietina	Species	Dermateaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	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
MIC	13

Activity Type	# Activity
Organism	13

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	128.0	ug.mL-1	PMID[523175]
NPT1101	Organism	Staphylococcus aureus subsp. aureus RN4220	Staphylococcus aureus subsp. aureus RN4220	MIC	=	4.0	ug.mL-1	PMID[523175]
NPT1101	Organism	Staphylococcus aureus subsp. aureus RN4220	Staphylococcus aureus subsp. aureus RN4220	MIC	=	128.0	ug.mL-1	PMID[523175]
NPT1101	Organism	Staphylococcus aureus subsp. aureus RN4220	Staphylococcus aureus subsp. aureus RN4220	MIC	=	4.0	ug.mL-1	PMID[523176]
NPT1101	Organism	Staphylococcus aureus subsp. aureus RN4220	Staphylococcus aureus subsp. aureus RN4220	MIC	=	32.0	ug.mL-1	PMID[523176]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	32.0	ug.mL-1	PMID[523177]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	1.0	ug.mL-1	PMID[523177]

☑ 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 NPC58001 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	207
0.1-0.2	1789
0.2-0.3	9802
0.3-0.4	24192
0.4-0.5	6055
0.5-0.6	586
0.6-0.7	28
0.7-0.8	32
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC314523
0.7656	Intermediate Similarity	NPC476829
0.764	Intermediate Similarity	NPC30527
0.7458	Intermediate Similarity	NPC211555
0.7452	Intermediate Similarity	NPC325683
0.744	Intermediate Similarity	NPC477219
0.7404	Intermediate Similarity	NPC37924
0.7401	Intermediate Similarity	NPC186452
0.7368	Intermediate Similarity	NPC476828
0.7311	Intermediate Similarity	NPC322800
0.7311	Intermediate Similarity	NPC477218
0.7311	Intermediate Similarity	NPC168135
0.7273	Intermediate Similarity	NPC476830
0.7264	Intermediate Similarity	NPC177432
0.7264	Intermediate Similarity	NPC299035
0.7238	Intermediate Similarity	NPC12660
0.7225	Intermediate Similarity	NPC476826
0.7225	Intermediate Similarity	NPC476827
0.7225	Intermediate Similarity	NPC476831
0.7204	Intermediate Similarity	NPC476832
0.7198	Intermediate Similarity	NPC54983
0.6866	Remote Similarity	NPC224395
0.6866	Remote Similarity	NPC208297
0.6816	Remote Similarity	NPC107458
0.6816	Remote Similarity	NPC295653
0.6748	Remote Similarity	NPC258022
0.67	Remote Similarity	NPC58112
0.67	Remote Similarity	NPC306300
0.67	Remote Similarity	NPC88938
0.665	Remote Similarity	NPC103452
0.665	Remote Similarity	NPC199461
0.665	Remote Similarity	NPC46313
0.6585	Remote Similarity	NPC289029
0.6585	Remote Similarity	NPC48323
0.6512	Remote Similarity	NPC309919
0.6504	Remote Similarity	NPC477586
0.6504	Remote Similarity	NPC477590
0.6504	Remote Similarity	NPC477588
0.6504	Remote Similarity	NPC477585
0.6443	Remote Similarity	NPC475455
0.6416	Remote Similarity	NPC477587
0.6416	Remote Similarity	NPC477589
0.621	Remote Similarity	NPC49195
0.6023	Remote Similarity	NPC120335
0.5876	Remote Similarity	NPC237219
0.5781	Remote Similarity	NPC50274
0.5753	Remote Similarity	NPC316403
0.5739	Remote Similarity	NPC309525
0.5721	Remote Similarity	NPC220408
0.5676	Remote Similarity	NPC314222
0.5676	Remote Similarity	NPC196449
0.5645	Remote Similarity	NPC472436
0.5636	Remote Similarity	NPC472287
0.5636	Remote Similarity	NPC472286
0.5625	Remote Similarity	NPC119481
0.5619	Remote Similarity	NPC475342
0.5617	Remote Similarity	NPC475196
0.5615	Remote Similarity	NPC165964
0.5614	Remote Similarity	NPC313804
0.5614	Remote Similarity	NPC315804
0.5607	Remote Similarity	NPC59827
0.5607	Remote Similarity	NPC184933
0.5605	Remote Similarity	NPC476514
0.5602	Remote Similarity	NPC316224

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 NPC58001 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	138
0.1-0.2	494
0.2-0.3	1885
0.3-0.4	4037
0.4-0.5	2419
0.5-0.6	170
0.6-0.7	6
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8626	High Similarity	NPD7896	Approved
0.6502	Remote Similarity	NPD6347	Phase 2
0.639	Remote Similarity	NPD7490	Discontinued
0.625	Remote Similarity	NPD6857	Phase 3
0.6227	Remote Similarity	NPD7180	Phase 3
0.6109	Remote Similarity	NPD6974	Phase 3
0.6096	Remote Similarity	NPD7031	Phase 1
0.6	Remote Similarity	NPD7547	Clinical (unspecified phase)
0.5973	Remote Similarity	NPD2433	Clinical (unspecified phase)
0.5939	Remote Similarity	NPD4898	Clinical (unspecified phase)
0.588	Remote Similarity	NPD7853	Phase 2
0.5856	Remote Similarity	NPD4667	Clinical (unspecified phase)
0.5844	Remote Similarity	NPD7284	Clinical (unspecified phase)
0.5823	Remote Similarity	NPD7022	Phase 2
0.5813	Remote Similarity	NPD2957	Phase 2
0.5808	Remote Similarity	NPD3263	Phase 3
0.5804	Remote Similarity	NPD5443	Clinical (unspecified phase)
0.5801	Remote Similarity	NPD1659	Phase 1
0.5787	Remote Similarity	NPD4368	Phase 2
0.5785	Remote Similarity	NPD1638	Discovery
0.5763	Remote Similarity	NPD4394	Clinical (unspecified phase)
0.5748	Remote Similarity	NPD772	Phase 3
0.5739	Remote Similarity	NPD5640	Discontinued
0.5721	Remote Similarity	NPD7811	Phase 3
0.5721	Remote Similarity	NPD7810	Phase 3
0.5714	Remote Similarity	NPD2779	Approved
0.5696	Remote Similarity	NPD6247	Clinical (unspecified phase)
0.567	Remote Similarity	NPD3945	Discontinued
0.5669	Remote Similarity	NPD5922	Phase 3
0.5636	Remote Similarity	NPD2951	Discontinued
0.5625	Remote Similarity	NPD5866	Approved
0.5622	Remote Similarity	NPD8104	Phase 3
0.5605	Remote Similarity	NPD3392	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