Structure

Physi-Chem Properties

Molecular Weight:  287.11
Volume:  247.682
LogP:  -1.417
LogD:  0.009
LogS:  -1.024
# Rotatable Bonds:  0
TPSA:  149.79
# H-Bond Aceptor:  9
# H-Bond Donor:  7
# Rings:  5
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.267
Synthetic Accessibility Score:  7.263
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:  -5.86
MDCK Permeability:  5.336022877600044e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.364
20% Bioavailability (F20%):  0.015
30% Bioavailability (F30%):  0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.065
Plasma Protein Binding (PPB):  17.546451568603516%
Volume Distribution (VD):  0.448
Pgp-substrate:  78.21709442138672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.014
CYP1A2-substrate:  0.195
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.526
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.027
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.202
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.064

ADMET: Excretion

Clearance (CL):  2.273
Half-life (T1/2):  0.582

ADMET: Toxicity

hERG Blockers:  0.053
Human Hepatotoxicity (H-HT):  0.083
Drug-inuced Liver Injury (DILI):  0.138
AMES Toxicity:  0.361
Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.007
Skin Sensitization:  0.182
Carcinogencity:  0.057
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.968

Download Data

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

  Natural Product: NPC139857

Natural Product ID:  NPC139857
Common Name*:   RMAHGNDIHNOZMD-LJQSUJOQSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RMAHGNDIHNOZMD-LJQSUJOQSA-N
Standard InCHI:  InChI=1S/C11H17N3O6/c1-2-4-3-7(16)13-9(12)14-10(3)6(15)5(2)20-11(18,19-4)8(10)17/h2-8,15-18H,1H3,(H3,12,13,14)/t2-,3-,4+,5-,6-,7-,8+,10-,11+/m1/s1
SMILES:  N=C1N[C@H](O)[C@@H]2[C@@]3(N1)[C@H](O)[C@H]1[C@@H]([C@@H]2O[C@@]([C@H]3O)(O1)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3233266
PubChem CID:   90669996
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]
NPO4175 Eremostachys loasifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17877 Knema austrosiamensis Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae 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]
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 = 400.0 nM PMID[482803]

☑ 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 NPC139857 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
0.9652 High Similarity NPC75839
0.9652 High Similarity NPC68327
0.704 Intermediate Similarity NPC121479
0.704 Intermediate Similarity NPC57436
0.6721 Remote Similarity NPC56298
0.6721 Remote Similarity NPC315036
0.6721 Remote Similarity NPC471628
0.6525 Remote Similarity NPC262050
0.6471 Remote Similarity NPC94319
0.6429 Remote Similarity NPC476967
0.6324 Remote Similarity NPC208118
0.6324 Remote Similarity NPC96080
0.6324 Remote Similarity NPC99905
0.6296 Remote Similarity NPC475887
0.6241 Remote Similarity NPC476497
0.6172 Remote Similarity NPC221148
0.617 Remote Similarity NPC476501
0.6154 Remote Similarity NPC317534
0.6115 Remote Similarity NPC20035
0.6084 Remote Similarity NPC309249
0.6083 Remote Similarity NPC470282
0.6029 Remote Similarity NPC476502
0.5896 Remote Similarity NPC139778
0.589 Remote Similarity NPC25455
0.589 Remote Similarity NPC15249
0.585 Remote Similarity NPC122819
0.5847 Remote Similarity NPC271772
0.5847 Remote Similarity NPC36927
0.5847 Remote Similarity NPC315969
0.584 Remote Similarity NPC315334
0.5839 Remote Similarity NPC297058
0.582 Remote Similarity NPC477060
0.582 Remote Similarity NPC123746
0.582 Remote Similarity NPC314408
0.582 Remote Similarity NPC314007
0.582 Remote Similarity NPC43850
0.5811 Remote Similarity NPC147753
0.5811 Remote Similarity NPC150057
0.5804 Remote Similarity NPC296686
0.5798 Remote Similarity NPC263058
0.5797 Remote Similarity NPC476955
0.5789 Remote Similarity NPC83047
0.5789 Remote Similarity NPC48127
0.5789 Remote Similarity NPC8009
0.5789 Remote Similarity NPC267217
0.5772 Remote Similarity NPC470284
0.5766 Remote Similarity NPC241597
0.5758 Remote Similarity NPC322449
0.5758 Remote Similarity NPC62845
0.5758 Remote Similarity NPC166242
0.5758 Remote Similarity NPC189854
0.5758 Remote Similarity NPC92874
0.5748 Remote Similarity NPC330590
0.5739 Remote Similarity NPC244539
0.5726 Remote Similarity NPC195969
0.5726 Remote Similarity NPC176381
0.5726 Remote Similarity NPC98750
0.5714 Remote Similarity NPC325900
0.5714 Remote Similarity NPC10897
0.5692 Remote Similarity NPC201712
0.569 Remote Similarity NPC313762
0.5683 Remote Similarity NPC313813
0.5682 Remote Similarity NPC239705
0.5682 Remote Similarity NPC314398
0.5682 Remote Similarity NPC314413
0.5678 Remote Similarity NPC70574
0.5658 Remote Similarity NPC287885
0.5652 Remote Similarity NPC28224
0.5649 Remote Similarity NPC475518
0.5643 Remote Similarity NPC221196
0.5643 Remote Similarity NPC39485
0.5629 Remote Similarity NPC474210
0.5625 Remote Similarity NPC155985
0.562 Remote Similarity NPC241959
0.5615 Remote Similarity NPC475249
0.561 Remote Similarity NPC313552
0.561 Remote Similarity NPC306838

  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 NPC139857 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
0.9483 High Similarity NPD577 Phase 3
0.9483 High Similarity NPD591 Approved
0.704 Intermediate Similarity NPD4833 Approved
0.704 Intermediate Similarity NPD35 Approved
0.6721 Remote Similarity NPD4835 Approved
0.6721 Remote Similarity NPD4838 Approved
0.6721 Remote Similarity NPD4837 Approved
0.6721 Remote Similarity NPD4836 Approved
0.6557 Remote Similarity NPD4282 Approved
0.6471 Remote Similarity NPD4827 Approved
0.6471 Remote Similarity NPD4828 Approved
0.6471 Remote Similarity NPD4826 Approved
0.6328 Remote Similarity NPD5376 Approved
0.6325 Remote Similarity NPD394 Phase 3
0.6316 Remote Similarity NPD3204 Clinical (unspecified phase)
0.6212 Remote Similarity NPD2690 Discontinued
0.6204 Remote Similarity NPD8347 Approved
0.6204 Remote Similarity NPD8346 Approved
0.6204 Remote Similarity NPD8345 Approved
0.6172 Remote Similarity NPD1450 Approved
0.6172 Remote Similarity NPD1449 Approved
0.5985 Remote Similarity NPD8174 Phase 2
0.5896 Remote Similarity NPD8087 Discontinued
0.5878 Remote Similarity NPD2700 Approved
0.5868 Remote Similarity NPD3200 Clinical (unspecified phase)
0.585 Remote Similarity NPD8449 Approved
0.582 Remote Similarity NPD3201 Approved
0.582 Remote Similarity NPD3203 Approved
0.582 Remote Similarity NPD3209 Approved
0.582 Remote Similarity NPD3208 Approved
0.582 Remote Similarity NPD3207 Approved
0.582 Remote Similarity NPD3202 Approved
0.5811 Remote Similarity NPD8450 Suspended
0.5797 Remote Similarity NPD4831 Approved
0.5797 Remote Similarity NPD4832 Approved
0.5797 Remote Similarity NPD4830 Approved
0.5766 Remote Similarity NPD3731 Phase 3
0.5748 Remote Similarity NPD5378 Approved
0.5748 Remote Similarity NPD5381 Approved
0.5748 Remote Similarity NPD5377 Approved
0.5726 Remote Similarity NPD5797 Approved
0.5726 Remote Similarity NPD5796 Clinical (unspecified phase)
0.5726 Remote Similarity NPD5798 Approved
0.5726 Remote Similarity NPD5795 Approved
0.5726 Remote Similarity NPD5794 Approved
0.5683 Remote Similarity NPD6940 Discontinued
0.5672 Remote Similarity NPD8307 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