Structure

Physi-Chem Properties

Molecular Weight:  438.06
Volume:  375.906
LogP:  -0.292
LogD:  -0.14
LogS:  -3.093
# Rotatable Bonds:  0
TPSA:  132.29
# H-Bond Aceptor:  9
# H-Bond Donor:  2
# Rings:  7
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.45
Synthetic Accessibility Score:  6.862
Fsp3:  0.722
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -5.12
MDCK Permeability:  8.35307491797721e-06
Pgp-inhibitor:  0.37
Pgp-substrate:  0.105
Human Intestinal Absorption (HIA):  0.118
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.181

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.013
Plasma Protein Binding (PPB):  45.408607482910156%
Volume Distribution (VD):  0.369
Pgp-substrate:  51.15839385986328%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.094
CYP2C19-inhibitor:  0.081
CYP2C19-substrate:  0.765
CYP2C9-inhibitor:  0.739
CYP2C9-substrate:  0.441
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.064
CYP3A4-inhibitor:  0.046
CYP3A4-substrate:  0.973

ADMET: Excretion

Clearance (CL):  7.473
Half-life (T1/2):  0.743

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.173
Drug-inuced Liver Injury (DILI):  0.995
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.964
Maximum Recommended Daily Dose:  0.082
Skin Sensitization:  0.4
Carcinogencity:  0.481
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.01

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

  Natural Product: NPC276822

Natural Product ID:  NPC276822
Common Name*:   NCDIBOQDVNONGL-HISJFFBUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NCDIBOQDVNONGL-HISJFFBUSA-N
Standard InCHI:  InChI=1S/C18H18N2O7S2/c21-8-1-2-9(22)12-6(8)4-17-16(27)20-13-7(10(23)3-11(24)14(13)25)5-18(20,29-28-17)15(26)19(12)17/h1-2,6-7,9,11-14,22,24-25H,3-5H2/t6-,7+,9+,11+,12+,13+,14+,17-,18-/m1/s1
SMILES:  C1=C[C@@H]([C@@H]2[C@H](C[C@@]34C(=O)N5[C@H]6[C@@H](C[C@]5(C(=O)N23)SS4)C(=O)C[C@@H]([C@@H]6O)O)C1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3102874
PubChem CID:   10410865
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002389] Diazinanes
        • [CHEMONTID:0000189] Piperazines
          • [CHEMONTID:0001731] Dioxopiperazines
            • [CHEMONTID:0003684] 2,5-dioxopiperazines
              • [CHEMONTID:0001732] Thiodioxopiperazines
                • [CHEMONTID:0001790] Epipolythiodioxopiperazines

*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
NPO21301 Stereum hirsutum Species Stereaceae Eukaryota n.a. n.a. n.a. PMID[12003003]
NPO21558 Ormosia sumatrana Species Fabaceae Eukaryota leaves n.a. n.a. PMID[15568789]
NPO19990 Axinyssa isabela Species Halichondriidae Eukaryota n.a. Isla Isabel (Gulf of California, Mexico) n.a. PMID[19007287]
NPO9838 Eucalyptus maideni Species Myrtaceae Eukaryota fresh leaves n.a. n.a. PMID[19778089]
NPO9838 Eucalyptus maideni Species Myrtaceae Eukaryota fresh fruits n.a. n.a. PMID[20092288]
NPO33508 Phoma sp. OUCMDZ-1847 Species Didymellaceae Eukaryota n.a. n.a. n.a. PMID[24370114]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. PMID[25565282]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota Mycelia n.a. n.a. PMID[26807743]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota Fruiting Bodies n.a. n.a. PMID[33246107]
NPO4994 Pachysandra procumbens Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[9784163]
NPO18460 Trema dielsiana Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18460 Trema dielsiana Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21301 Stereum hirsutum Species Stereaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21301 Stereum hirsutum Species Stereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17541 Andryala pinnatifida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18857 Pteronia eenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20485 Cussonia arborea Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9838 Eucalyptus maideni Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20276 Burasaia madagascariensis Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18460 Trema dielsiana Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13404 Plantago subulata Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20747 Stictocardia campanulata Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21238 Berberis tabiensis Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19796 Azolla filiculoides Species Azollaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19907 Helicobasidium mompa Species Helicobasidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18114 Cyclamen repandum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21490 Hypoxylon fragiforme Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24508 Aspergillus brunneus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19031 Thymus marschallianus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19990 Axinyssa isabela Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4994 Pachysandra procumbens Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21558 Ormosia sumatrana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21431 Rapanea laetevirens Species Primulaceae 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT3140 Cell Line MGC-803 Homo sapiens IC50 = 3400.0 nM PMID[557236]
NPT111 Cell Line K562 Homo sapiens IC50 > 10000.0 nM PMID[557236]
NPT81 Cell Line A549 Homo sapiens IC50 > 10000.0 nM PMID[557236]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 7100.0 nM PMID[557236]
NPT116 Cell Line HL-60 Homo sapiens IC50 = 3500.0 nM PMID[557236]

☑ 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 NPC276822 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
0.8647 High Similarity NPC247902
0.8647 High Similarity NPC262880
0.8248 Intermediate Similarity NPC25327
0.8058 Intermediate Similarity NPC41162
0.7857 Intermediate Similarity NPC8325
0.7744 Intermediate Similarity NPC309731
0.7635 Intermediate Similarity NPC469800
0.7372 Intermediate Similarity NPC271115
0.7357 Intermediate Similarity NPC266910
0.732 Intermediate Similarity NPC243412
0.7194 Intermediate Similarity NPC28542
0.7174 Intermediate Similarity NPC272166
0.7063 Intermediate Similarity NPC475342
0.7055 Intermediate Similarity NPC220396
0.6849 Remote Similarity NPC211848
0.6783 Remote Similarity NPC17581
0.6783 Remote Similarity NPC476155
0.6761 Remote Similarity NPC66007
0.6736 Remote Similarity NPC470788
0.6732 Remote Similarity NPC82129
0.6622 Remote Similarity NPC97580
0.6549 Remote Similarity NPC314550
0.6467 Remote Similarity NPC309525
0.6438 Remote Similarity NPC470300
0.6346 Remote Similarity NPC99864
0.6282 Remote Similarity NPC120420
0.6188 Remote Similarity NPC88943
0.6178 Remote Similarity NPC313348
0.6178 Remote Similarity NPC475987
0.6164 Remote Similarity NPC45813
0.6154 Remote Similarity NPC120335
0.6101 Remote Similarity NPC477400
0.6071 Remote Similarity NPC100810
0.6071 Remote Similarity NPC144714
0.6037 Remote Similarity NPC956
0.6012 Remote Similarity NPC477399
0.6012 Remote Similarity NPC477401
0.5988 Remote Similarity NPC473955
0.5987 Remote Similarity NPC315188
0.5972 Remote Similarity NPC176773
0.5957 Remote Similarity NPC188785
0.5931 Remote Similarity NPC207820
0.5924 Remote Similarity NPC470539
0.5903 Remote Similarity NPC472856
0.5897 Remote Similarity NPC476951
0.5894 Remote Similarity NPC471673
0.5874 Remote Similarity NPC476877
0.5867 Remote Similarity NPC288629
0.5857 Remote Similarity NPC91036
0.5833 Remote Similarity NPC133420
0.5817 Remote Similarity NPC477143
0.5817 Remote Similarity NPC477140
0.5799 Remote Similarity NPC15440
0.5799 Remote Similarity NPC264958
0.5799 Remote Similarity NPC185590
0.5793 Remote Similarity NPC476876
0.5793 Remote Similarity NPC25025
0.5789 Remote Similarity NPC96731
0.5782 Remote Similarity NPC274895
0.5779 Remote Similarity NPC160688
0.5778 Remote Similarity NPC324506
0.5771 Remote Similarity NPC322372
0.5771 Remote Similarity NPC319334
0.5771 Remote Similarity NPC327517
0.5769 Remote Similarity NPC36254
0.5758 Remote Similarity NPC315848
0.5758 Remote Similarity NPC315210
0.5753 Remote Similarity NPC271562
0.5747 Remote Similarity NPC477398
0.5723 Remote Similarity NPC164476
0.5723 Remote Similarity NPC471471
0.5723 Remote Similarity NPC121601
0.5714 Remote Similarity NPC13351
0.5686 Remote Similarity NPC235625
0.5686 Remote Similarity NPC471109
0.5686 Remote Similarity NPC474006
0.568 Remote Similarity NPC471680
0.5673 Remote Similarity NPC475609
0.5669 Remote Similarity NPC470654
0.5669 Remote Similarity NPC470650
0.5669 Remote Similarity NPC470653
0.5665 Remote Similarity NPC315809
0.5665 Remote Similarity NPC314050
0.5638 Remote Similarity NPC473232
0.5616 Remote Similarity NPC87919
0.5615 Remote Similarity NPC166169
0.5614 Remote Similarity NPC266697
0.56 Remote Similarity NPC476875

  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 NPC276822 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
0.7174 Intermediate Similarity NPD1000 Clinical (unspecified phase)
0.6346 Remote Similarity NPD8415 Approved
0.6306 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5939 Remote Similarity NPD5193 Discontinued
0.5839 Remote Similarity NPD1376 Discontinued
0.5747 Remote Similarity NPD8414 Discontinued
0.5732 Remote Similarity NPD3677 Clinical (unspecified phase)
0.5723 Remote Similarity NPD8384 Approved
0.5714 Remote Similarity NPD2645 Approved
0.5649 Remote Similarity NPD3159 Discontinued

  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