Structure

Physi-Chem Properties

Molecular Weight:  389.98
Volume:  319.823
LogP:  -0.358
LogD:  0.754
LogS:  -3.931
# Rotatable Bonds:  1
TPSA:  81.08
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.642
Synthetic Accessibility Score:  6.573
Fsp3:  0.538
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.357
MDCK Permeability:  1.9167315258528106e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.412
20% Bioavailability (F20%):  0.148
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.144
Plasma Protein Binding (PPB):  40.811737060546875%
Volume Distribution (VD):  0.594
Pgp-substrate:  44.35294723510742%

ADMET: Metabolism

CYP1A2-inhibitor:  0.156
CYP1A2-substrate:  0.097
CYP2C19-inhibitor:  0.986
CYP2C19-substrate:  0.89
CYP2C9-inhibitor:  0.942
CYP2C9-substrate:  0.107
CYP2D6-inhibitor:  0.21
CYP2D6-substrate:  0.062
CYP3A4-inhibitor:  0.086
CYP3A4-substrate:  0.971

ADMET: Excretion

Clearance (CL):  7.618
Half-life (T1/2):  0.4

ADMET: Toxicity

hERG Blockers:  0.062
Human Hepatotoxicity (H-HT):  0.097
Drug-inuced Liver Injury (DILI):  0.938
AMES Toxicity:  0.056
Rat Oral Acute Toxicity:  0.894
Maximum Recommended Daily Dose:  0.888
Skin Sensitization:  0.932
Carcinogencity:  0.733
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.948

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

  Natural Product: NPC66007

Natural Product ID:  NPC66007
Common Name*:   Gliotoxin G
IUPAC Name:   n.a.
Synonyms:   Gliotoxin G
Standard InCHIKey:  TZBWGHOEGGDHNR-RBJBARPLSA-N
Standard InCHI:  InChI=1S/C13H14N2O4S4/c1-14-10(18)12-5-7-3-2-4-8(17)9(7)15(12)11(19)13(14,6-16)21-23-22-20-12/h2-4,8-9,16-17H,5-6H2,1H3/t8-,9-,12+,13+/m0/s1
SMILES:  CN1C(=O)[C@]23CC4=CC=C[C@@H]([C@H]4N2C(=O)[C@@]1(CO)SSSS3)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1950962
PubChem CID:   3007092
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives

*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
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[10479323]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12350167]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[14640527]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota Axinella verrucosa Mediterranean n.a. PMID[14738391]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15043411]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Sussex Inlet, New South Wales, Australia n.a. PMID[15104517]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15332862]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Berkeley Pit lake n.a. PMID[17970594]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. New Zealand n.a. PMID[19323568]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19326880]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20452770]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. North Sea n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Limonium tubiflorum n.a. PMID[21146414]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21916432]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22148349]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22458669]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23360521]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23477451]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23603293]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23972215]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24033077]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24437979]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[31433188]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[9392888]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[Article]

☑ 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT168 Cell Line P388 Mus musculus IC50 = 20.0 nM PMID[448968]
NPT5 Individual Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens IC50 = 2100.0 nM PMID[448968]

☑ 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 NPC66007 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9358 High Similarity NPC272166
0.9107 High Similarity NPC476155
0.9107 High Similarity NPC17581
0.8291 Intermediate Similarity NPC470300
0.8182 Intermediate Similarity NPC97580
0.8067 Intermediate Similarity NPC470788
0.7209 Intermediate Similarity NPC262880
0.7209 Intermediate Similarity NPC247902
0.7176 Intermediate Similarity NPC41162
0.7034 Intermediate Similarity NPC475342
0.6761 Remote Similarity NPC276822
0.6723 Remote Similarity NPC188785
0.6667 Remote Similarity NPC82129
0.6587 Remote Similarity NPC314550
0.6577 Remote Similarity NPC475975
0.6377 Remote Similarity NPC120335
0.637 Remote Similarity NPC471680
0.6341 Remote Similarity NPC476877
0.6296 Remote Similarity NPC36254
0.624 Remote Similarity NPC476876
0.6218 Remote Similarity NPC313265
0.6194 Remote Similarity NPC315188
0.6183 Remote Similarity NPC288629
0.6167 Remote Similarity NPC469739
0.6121 Remote Similarity NPC324506
0.6018 Remote Similarity NPC277341
0.6018 Remote Similarity NPC226982
0.6014 Remote Similarity NPC309525
0.6 Remote Similarity NPC469455
0.6 Remote Similarity NPC476875
0.5923 Remote Similarity NPC251122
0.5891 Remote Similarity NPC207820
0.5873 Remote Similarity NPC473289
0.585 Remote Similarity NPC25025
0.5833 Remote Similarity NPC166169
0.5821 Remote Similarity NPC271115
0.5814 Remote Similarity NPC271562
0.5804 Remote Similarity NPC469666
0.5797 Remote Similarity NPC302169
0.5794 Remote Similarity NPC77703
0.5789 Remote Similarity NPC309731
0.5786 Remote Similarity NPC474082
0.5786 Remote Similarity NPC175726
0.5781 Remote Similarity NPC133420
0.5778 Remote Similarity NPC28542
0.5769 Remote Similarity NPC474099
0.5745 Remote Similarity NPC476951
0.5735 Remote Similarity NPC471673
0.5733 Remote Similarity NPC309450
0.5733 Remote Similarity NPC247776
0.5733 Remote Similarity NPC475266
0.5733 Remote Similarity NPC304299
0.5733 Remote Similarity NPC475278
0.5731 Remote Similarity NPC302235
0.5705 Remote Similarity NPC315210
0.5705 Remote Similarity NPC315848
0.5702 Remote Similarity NPC471768
0.5695 Remote Similarity NPC470301
0.5683 Remote Similarity NPC273185
0.5664 Remote Similarity NPC25327
0.5664 Remote Similarity NPC8325
0.5652 Remote Similarity NPC209232
0.5649 Remote Similarity NPC476276
0.5629 Remote Similarity NPC71866
0.5625 Remote Similarity NPC475149
0.5625 Remote Similarity NPC471097
0.5612 Remote Similarity NPC266910
0.5612 Remote Similarity NPC160688
0.5608 Remote Similarity NPC248283

  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 NPC66007 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.9358 High Similarity NPD1000 Clinical (unspecified phase)
0.5786 Remote Similarity NPD8273 Phase 1
0.5766 Remote Similarity NPD2645 Approved
0.5736 Remote Similarity NPD7333 Discontinued
0.5693 Remote Similarity NPD3159 Discontinued
0.5683 Remote Similarity NPD1806 Approved
0.5672 Remote Similarity NPD1376 Discontinued
0.5655 Remote Similarity NPD5263 Approved
0.5638 Remote Similarity NPD8172 Phase 2
0.5638 Remote Similarity NPD6073 Approved
0.5638 Remote Similarity NPD8173 Phase 2
0.5603 Remote Similarity NPD4706 Clinical (unspecified phase)

  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