Structure

Physi-Chem Properties

Molecular Weight:  303.11
Volume:  256.472
LogP:  -1.727
LogD:  -0.559
LogS:  -1.477
# Rotatable Bonds:  0
TPSA:  170.02
# H-Bond Aceptor:  10
# H-Bond Donor:  8
# Rings:  5
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.233
Synthetic Accessibility Score:  7.038
Fsp3:  0.909
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.108
MDCK Permeability:  8.193695248337463e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.16
20% Bioavailability (F20%):  0.219
30% Bioavailability (F30%):  0.947

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.092
Plasma Protein Binding (PPB):  18.475048065185547%
Volume Distribution (VD):  0.425
Pgp-substrate:  79.31236267089844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.004
CYP1A2-substrate:  0.606
CYP2C19-inhibitor:  0.017
CYP2C19-substrate:  0.121
CYP2C9-inhibitor:  0.018
CYP2C9-substrate:  0.023
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.137
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.025

ADMET: Excretion

Clearance (CL):  1.785
Half-life (T1/2):  0.723

ADMET: Toxicity

hERG Blockers:  0.052
Human Hepatotoxicity (H-HT):  0.057
Drug-inuced Liver Injury (DILI):  0.531
AMES Toxicity:  0.369
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.123
Carcinogencity:  0.025
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.201

Download Data

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

  Natural Product: NPC75839

Natural Product ID:  NPC75839
Common Name*:   XXUFXWUHBMGUMY-QOZOJKKESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XXUFXWUHBMGUMY-QOZOJKKESA-N
Standard InCHI:  InChI=1S/C11H17N3O7/c1-9(18)4-2-6(16)13-8(12)14-10(2)3(15)5(9)21-11(19,20-4)7(10)17/h2-7,15-19H,1H3,(H3,12,13,14)/t2-,3-,4-,5+,6-,7+,9+,10-,11+/m1/s1
SMILES:  N=C1N[C@H](O)[C@@H]2[C@@]3(N1)[C@H](O)[C@H]1[C@@]([C@@H]2O[C@@]([C@H]3O)(O1)O)(C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3233265
PubChem CID:   90669995
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0004788] Diazanaphthalenes
        • [CHEMONTID:0004789] Benzodiazines
          • [CHEMONTID:0000485] Quinazolines

*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
NPO19150 Swertia hookeri Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(80)85027-8]
NPO19685 Streptomyces cyanogenus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[21188999]
NPO40767 Pufferfish takifugu Species n.a. n.a. n.a. n.a. n.a. PMID[24654947]
NPO19353 Tadehagi triquetrum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[27100993]
NPO19353 Tadehagi triquetrum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19353 Tadehagi triquetrum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19353 Tadehagi triquetrum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16257 Andromeda japonica Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15493 Streptomyces sannurensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4175 Eremostachys loasifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23947 Boehmeria excelsa Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17877 Knema austrosiamensis Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19892 Geranium onoei Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23719 Senecio cachinalensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9521 Viguiera schultzii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7687 Bistorta affinis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19685 Streptomyces cyanogenus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19150 Swertia hookeri Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24161 Acremonium loliae Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16383 Androstachys johnsonii Species Picrodendraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9186 Cestrum euanthes Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19353 Tadehagi triquetrum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18990 Plagiorhegma dubium Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14598 Alternaria eichhorniae Species Pleosporaceae 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
NPT2 Others Unspecified EC50 = 130.0 nM PMID[504449]

☑ 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 NPC75839 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
0.9655 High Similarity NPC68327
0.9652 High Similarity NPC139857
0.7063 Intermediate Similarity NPC121479
0.7063 Intermediate Similarity NPC57436
0.6748 Remote Similarity NPC56298
0.6748 Remote Similarity NPC471628
0.6613 Remote Similarity NPC315036
0.6496 Remote Similarity NPC94319
0.6434 Remote Similarity NPC262050
0.6338 Remote Similarity NPC476967
0.6324 Remote Similarity NPC475887
0.6232 Remote Similarity NPC99905
0.6232 Remote Similarity NPC208118
0.6232 Remote Similarity NPC96080
0.6154 Remote Similarity NPC476497
0.6084 Remote Similarity NPC476501
0.6077 Remote Similarity NPC221148
0.6028 Remote Similarity NPC20035
0.6 Remote Similarity NPC309249
0.5984 Remote Similarity NPC470282
0.5942 Remote Similarity NPC476502
0.594 Remote Similarity NPC317534
0.5809 Remote Similarity NPC139778
0.5797 Remote Similarity NPC241597
0.5772 Remote Similarity NPC122819
0.5762 Remote Similarity NPC297058
0.575 Remote Similarity NPC271772
0.575 Remote Similarity NPC36927
0.575 Remote Similarity NPC315969
0.5748 Remote Similarity NPC315334
0.5733 Remote Similarity NPC150057
0.5733 Remote Similarity NPC147753
0.5726 Remote Similarity NPC313762
0.5726 Remote Similarity NPC314408
0.5726 Remote Similarity NPC123746
0.5726 Remote Similarity NPC477060
0.5726 Remote Similarity NPC43850
0.5726 Remote Similarity NPC314007
0.5714 Remote Similarity NPC476955
0.5705 Remote Similarity NPC25455
0.5705 Remote Similarity NPC15249
0.5704 Remote Similarity NPC48127
0.5704 Remote Similarity NPC8009
0.5704 Remote Similarity NPC267217
0.5704 Remote Similarity NPC83047
0.5702 Remote Similarity NPC263058
0.568 Remote Similarity NPC470284
0.5672 Remote Similarity NPC189854
0.5672 Remote Similarity NPC92874
0.5672 Remote Similarity NPC62845
0.5672 Remote Similarity NPC166242
0.5672 Remote Similarity NPC322449
0.5659 Remote Similarity NPC330590
0.5641 Remote Similarity NPC244539
0.5635 Remote Similarity NPC195969
0.5635 Remote Similarity NPC176381
0.563 Remote Similarity NPC98750
0.563 Remote Similarity NPC325900
0.563 Remote Similarity NPC10897
0.5616 Remote Similarity NPC296686
0.5603 Remote Similarity NPC313813

  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 NPC75839 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
0.9826 High Similarity NPD591 Approved
0.9826 High Similarity NPD577 Phase 3
0.7063 Intermediate Similarity NPD4833 Approved
0.7063 Intermediate Similarity NPD35 Approved
0.6748 Remote Similarity NPD4838 Approved
0.6748 Remote Similarity NPD4837 Approved
0.6748 Remote Similarity NPD4836 Approved
0.6748 Remote Similarity NPD4835 Approved
0.6585 Remote Similarity NPD4282 Approved
0.6496 Remote Similarity NPD4827 Approved
0.6496 Remote Similarity NPD4828 Approved
0.6496 Remote Similarity NPD4826 Approved
0.6357 Remote Similarity NPD5376 Approved
0.6356 Remote Similarity NPD394 Phase 3
0.6232 Remote Similarity NPD8345 Approved
0.6232 Remote Similarity NPD8347 Approved
0.6232 Remote Similarity NPD8346 Approved
0.6119 Remote Similarity NPD2690 Discontinued
0.6103 Remote Similarity NPD3204 Clinical (unspecified phase)
0.6077 Remote Similarity NPD1450 Approved
0.6077 Remote Similarity NPD1449 Approved
0.5926 Remote Similarity NPD8087 Discontinued
0.5827 Remote Similarity NPD4830 Approved
0.5827 Remote Similarity NPD4831 Approved
0.5827 Remote Similarity NPD4832 Approved
0.5797 Remote Similarity NPD3731 Phase 3
0.5778 Remote Similarity NPD8174 Phase 2
0.5772 Remote Similarity NPD8449 Approved
0.5772 Remote Similarity NPD3200 Clinical (unspecified phase)
0.5733 Remote Similarity NPD8450 Suspended
0.5726 Remote Similarity NPD3209 Approved
0.5726 Remote Similarity NPD3203 Approved
0.5726 Remote Similarity NPD3201 Approved
0.5726 Remote Similarity NPD3207 Approved
0.5726 Remote Similarity NPD3208 Approved
0.5726 Remote Similarity NPD3202 Approved
0.5704 Remote Similarity NPD8307 Discontinued
0.5672 Remote Similarity NPD2700 Approved
0.5659 Remote Similarity NPD5377 Approved
0.5659 Remote Similarity NPD5381 Approved
0.5659 Remote Similarity NPD5378 Approved
0.5635 Remote Similarity NPD5798 Approved
0.5635 Remote Similarity NPD5794 Approved
0.5635 Remote Similarity NPD5797 Approved
0.5635 Remote Similarity NPD5796 Clinical (unspecified phase)
0.5635 Remote Similarity NPD5795 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