Structure

Physi-Chem Properties

Molecular Weight:  195.08
Volume:  174.534
LogP:  -1.15
LogD:  -0.328
LogS:  -2.96
# Rotatable Bonds:  0
TPSA:  99.43
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.47
Synthetic Accessibility Score:  3.334
Fsp3:  0.286
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.592
MDCK Permeability:  3.229067078791559e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.989
Human Intestinal Absorption (HIA):  0.962
20% Bioavailability (F20%):  0.038
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.755
Plasma Protein Binding (PPB):  45.20794677734375%
Volume Distribution (VD):  1.249
Pgp-substrate:  49.593414306640625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.03
CYP1A2-substrate:  0.971
CYP2C19-inhibitor:  0.073
CYP2C19-substrate:  0.054
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.036
CYP2D6-inhibitor:  0.033
CYP2D6-substrate:  0.117
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.212

ADMET: Excretion

Clearance (CL):  4.907
Half-life (T1/2):  0.914

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.78
Drug-inuced Liver Injury (DILI):  0.892
AMES Toxicity:  0.026
Rat Oral Acute Toxicity:  0.762
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.032
Carcinogencity:  0.075
Eye Corrosion:  0.003
Eye Irritation:  0.074
Respiratory Toxicity:  0.947

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

  Natural Product: NPC476561

Natural Product ID:  NPC476561
Common Name*:   QNNJWRQCDFPIQY-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QNNJWRQCDFPIQY-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H9N5O2.ClH/c1-11-4(8)3-5(10-7(11)14)12(2)6(13)9-3;/h8H,1-2H3,(H,9,13)(H,10,14);1H
SMILES:  CN1C(=[NH2+])C2=C(NC1=O)N(C)C(=O)N2.[Cl-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001797] Imidazopyrimidines
        • [CHEMONTID:0000245] Purines and purine derivatives
          • [CHEMONTID:0000597] Purinones

*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
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. Iojima Island, the Satsunan Islands, southern Japan (3047 N; 13017 E) n.a. PMID[15497958]
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[17067172]
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. Republic of Palau 2006; 2007 PMID[20681583]
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[28207259]
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[7714542]
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[9599281]

☑ 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
NPT1788 Individual Protein Alpha-1a adrenergic receptor Homo sapiens Ki = 885 nM PMID[20681583]
NPT1789 Individual Protein Alpha-1b adrenergic receptor Homo sapiens Ki = 758 nM PMID[20681583]
NPT221 Individual Protein Alpha-1d adrenergic receptor Homo sapiens Ki = 497 nM PMID[20681583]
NPT2776 Individual Protein Serotonin 1e (5-HT1e) receptor Homo sapiens Ki = 2900 nM PMID[20681583]
NPT272 Individual Protein Kappa opioid receptor Homo sapiens Ki = 1800 nM PMID[20681583]
NPT145 Individual Protein Mu opioid receptor Homo sapiens Ki = 8900 nM PMID[20681583]
NPT3743 Individual Protein Glutamate receptor ionotropic, AMPA 4 Homo sapiens Activity = 100 % PMID[20681583]
NPT3742 Individual Protein Glutamate receptor ionotropic, AMPA 2 Homo sapiens Activity = 99 % PMID[20681583]
NPT32 Organism Mus musculus Mus musculus Activity = 2.4 nmol PMID[20681583]
NPT2 Others Unspecified Activity = 0.9 Hz PMID[20681583]
NPT2 Others Unspecified Activity = 3.6 Hz PMID[20681583]
NPT2 Others Unspecified Activity = 6 Hz PMID[20681583]
NPT2 Others Unspecified Activity = 0.95 Hz PMID[20681583]
NPT2 Others Unspecified Inhibition = 32 % PMID[20681583]
NPT2 Others Unspecified Inhibition = 29.6 % PMID[20681583]
NPT2 Others Unspecified Inhibition = 22 % PMID[20681583]
NPT2 Others Unspecified Inhibition = 71 % PMID[20681583]
NPT423 Protein Complex Neuronal acetylcholine receptor; alpha3/beta2 Homo sapiens Ki = 4200 nM PMID[20681583]
NPT999 Protein Complex GABA-A receptor; alpha-1/beta-3/gamma-2 Homo sapiens Activity = 99 % PMID[20681583]
NPT1002 Protein Complex GABA A receptor alpha-4/beta-3/gamma-2 Homo sapiens Activity = 93 % PMID[20681583]

☑ 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 NPC476561 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
0.9388 High Similarity NPC476562
0.8812 High Similarity NPC476099
0.8269 Intermediate Similarity NPC476564
0.8241 Intermediate Similarity NPC303899
0.8198 Intermediate Similarity NPC158847
0.8 Intermediate Similarity NPC10466
0.787 Intermediate Similarity NPC75131
0.7807 Intermediate Similarity NPC252603
0.7748 Intermediate Similarity NPC256849
0.7685 Intermediate Similarity NPC119133
0.7679 Intermediate Similarity NPC199790
0.7611 Intermediate Similarity NPC148385
0.7589 Intermediate Similarity NPC41958
0.7568 Intermediate Similarity NPC47936
0.7568 Intermediate Similarity NPC4837
0.7568 Intermediate Similarity NPC312187
0.7478 Intermediate Similarity NPC278549
0.7477 Intermediate Similarity NPC174114
0.7477 Intermediate Similarity NPC87981
0.7395 Intermediate Similarity NPC109322
0.7333 Intermediate Similarity NPC180493
0.7117 Intermediate Similarity NPC18335
0.704 Intermediate Similarity NPC104011
0.6942 Remote Similarity NPC139776
0.6909 Remote Similarity NPC293163
0.6905 Remote Similarity NPC246193
0.6881 Remote Similarity NPC320256
0.6875 Remote Similarity NPC59314
0.6774 Remote Similarity NPC248007
0.6759 Remote Similarity NPC51000
0.6641 Remote Similarity NPC287876
0.6639 Remote Similarity NPC327579
0.6562 Remote Similarity NPC14330
0.6538 Remote Similarity NPC57279
0.65 Remote Similarity NPC313547
0.648 Remote Similarity NPC5707
0.6475 Remote Similarity NPC189314
0.6475 Remote Similarity NPC68938
0.6408 Remote Similarity NPC321052
0.6391 Remote Similarity NPC320818
0.6324 Remote Similarity NPC317821
0.6296 Remote Similarity NPC33996
0.625 Remote Similarity NPC129756
0.6207 Remote Similarity NPC273327
0.6204 Remote Similarity NPC76544
0.6204 Remote Similarity NPC167285
0.6204 Remote Similarity NPC209525
0.6204 Remote Similarity NPC161659
0.6204 Remote Similarity NPC226184
0.6165 Remote Similarity NPC324009
0.6121 Remote Similarity NPC187191
0.6121 Remote Similarity NPC326248
0.6119 Remote Similarity NPC319221
0.6115 Remote Similarity NPC229974
0.6115 Remote Similarity NPC314152
0.6106 Remote Similarity NPC9639
0.6099 Remote Similarity NPC189068
0.6099 Remote Similarity NPC164665
0.6098 Remote Similarity NPC327613
0.6056 Remote Similarity NPC309832
0.6056 Remote Similarity NPC219313
0.605 Remote Similarity NPC155498
0.6028 Remote Similarity NPC21448
0.6028 Remote Similarity NPC156461
0.6028 Remote Similarity NPC107374
0.5972 Remote Similarity NPC136349
0.5956 Remote Similarity NPC262926
0.5952 Remote Similarity NPC240084
0.5944 Remote Similarity NPC269827
0.592 Remote Similarity NPC63433
0.5912 Remote Similarity NPC61198
0.5903 Remote Similarity NPC121222
0.5882 Remote Similarity NPC111132
0.5822 Remote Similarity NPC150853
0.58 Remote Similarity NPC239737
0.5786 Remote Similarity NPC296437
0.5782 Remote Similarity NPC211025
0.5782 Remote Similarity NPC85689
0.5782 Remote Similarity NPC185991
0.5782 Remote Similarity NPC161224
0.5762 Remote Similarity NPC195140
0.5745 Remote Similarity NPC470266
0.5743 Remote Similarity NPC472816
0.5743 Remote Similarity NPC321814
0.5743 Remote Similarity NPC328479
0.5734 Remote Similarity NPC217656
0.5705 Remote Similarity NPC130586
0.5705 Remote Similarity NPC164952
0.5705 Remote Similarity NPC302778
0.5705 Remote Similarity NPC212551
0.5704 Remote Similarity NPC186619
0.5694 Remote Similarity NPC274384
0.5694 Remote Similarity NPC89147
0.5667 Remote Similarity NPC174802
0.5667 Remote Similarity NPC472834
0.5664 Remote Similarity NPC476528
0.5664 Remote Similarity NPC476433
0.5655 Remote Similarity NPC197068
0.5629 Remote Similarity NPC224076
0.5625 Remote Similarity NPC318590
0.5625 Remote Similarity NPC476013
0.5625 Remote Similarity NPC211820
0.5625 Remote Similarity NPC476520
0.5625 Remote Similarity NPC251233
0.5625 Remote Similarity NPC476522
0.5625 Remote Similarity NPC474986
0.5616 Remote Similarity NPC476408

  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 NPC476561 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
0.7807 Intermediate Similarity NPD76 Approved
0.7807 Intermediate Similarity NPD9288 Approved
0.7807 Intermediate Similarity NPD9292 Approved
0.7807 Intermediate Similarity NPD9289 Approved
0.7748 Intermediate Similarity NPD9358 Approved
0.7748 Intermediate Similarity NPD9359 Approved
0.7685 Intermediate Similarity NPD9291 Approved
0.7479 Intermediate Similarity NPD579 Clinical (unspecified phase)
0.7414 Intermediate Similarity NPD9360 Approved
0.735 Intermediate Similarity NPD580 Discontinued
0.7333 Intermediate Similarity NPD78 Approved
0.7333 Intermediate Similarity NPD9544 Approved
0.7304 Intermediate Similarity NPD9086 Approved
0.7273 Intermediate Similarity NPD281 Approved
0.7265 Intermediate Similarity NPD237 Clinical (unspecified phase)
0.7227 Intermediate Similarity NPD2221 Clinical (unspecified phase)
0.7167 Intermediate Similarity NPD4262 Discontinued
0.7154 Intermediate Similarity NPD1128 Approved
0.7154 Intermediate Similarity NPD1127 Approved
0.7119 Intermediate Similarity NPD578 Discontinued
0.7117 Intermediate Similarity NPD8836 Approved
0.6984 Remote Similarity NPD282 Approved
0.6983 Remote Similarity NPD9373 Approved
0.6957 Remote Similarity NPD8955 Approved
0.6957 Remote Similarity NPD8954 Approved
0.6935 Remote Similarity NPD1775 Approved
0.6935 Remote Similarity NPD1085 Approved
0.6875 Remote Similarity NPD8837 Clinical (unspecified phase)
0.6864 Remote Similarity NPD9374 Approved
0.6842 Remote Similarity NPD1117 Clinical (unspecified phase)
0.6822 Remote Similarity NPD1119 Phase 2
0.6818 Remote Similarity NPD1118 Discontinued
0.6774 Remote Similarity NPD9084 Phase 2
0.6759 Remote Similarity NPD8838 Approved
0.6752 Remote Similarity NPD9375 Discontinued
0.6746 Remote Similarity NPD870 Clinical (unspecified phase)
0.672 Remote Similarity NPD9408 Phase 3
0.6694 Remote Similarity NPD9606 Approved
0.6693 Remote Similarity NPD9633 Phase 3
0.6642 Remote Similarity NPD7531 Clinical (unspecified phase)
0.6641 Remote Similarity NPD8829 Clinical (unspecified phase)
0.6639 Remote Similarity NPD9607 Approved
0.6639 Remote Similarity NPD307 Approved
0.6585 Remote Similarity NPD9290 Approved
0.6585 Remote Similarity NPD9409 Discontinued
0.6583 Remote Similarity NPD757 Phase 3
0.6522 Remote Similarity NPD9626 Clinical (unspecified phase)
0.6519 Remote Similarity NPD2253 Discontinued
0.6515 Remote Similarity NPD535 Approved
0.6512 Remote Similarity NPD248 Discontinued
0.6489 Remote Similarity NPD9083 Clinical (unspecified phase)
0.648 Remote Similarity NPD8830 Phase 3
0.6475 Remote Similarity NPD8833 Approved
0.6475 Remote Similarity NPD8831 Approved
0.6471 Remote Similarity NPD2179 Discontinued
0.6331 Remote Similarity NPD1730 Discontinued
0.6316 Remote Similarity NPD9484 Clinical (unspecified phase)
0.6279 Remote Similarity NPD515 Phase 1
0.6271 Remote Similarity NPD1816 Clinical (unspecified phase)
0.6268 Remote Similarity NPD3708 Phase 2
0.6241 Remote Similarity NPD4183 Phase 3
0.6241 Remote Similarity NPD4182 Phase 3
0.6204 Remote Similarity NPD3696 Approved
0.6204 Remote Similarity NPD3695 Approved
0.6204 Remote Similarity NPD193 Suspended
0.6148 Remote Similarity NPD1121 Approved
0.6148 Remote Similarity NPD1120 Approved
0.6119 Remote Similarity NPD1058 Discontinued
0.6115 Remote Similarity NPD185 Approved
0.608 Remote Similarity NPD1368 Approved
0.6071 Remote Similarity NPD4240 Approved
0.6058 Remote Similarity NPD1808 Phase 1
0.6048 Remote Similarity NPD9584 Phase 2
0.6045 Remote Similarity NPD547 Clinical (unspecified phase)
0.6045 Remote Similarity NPD545 Clinical (unspecified phase)
0.604 Remote Similarity NPD5321 Phase 3
0.6028 Remote Similarity NPD250 Approved
0.6028 Remote Similarity NPD166 Approved
0.6028 Remote Similarity NPD7158 Phase 1
0.6028 Remote Similarity NPD249 Approved
0.6017 Remote Similarity NPD341 Approved
0.6017 Remote Similarity NPD340 Approved
0.6 Remote Similarity NPD9102 Approved
0.6 Remote Similarity NPD9103 Approved
0.5972 Remote Similarity NPD548 Clinical (unspecified phase)
0.5957 Remote Similarity NPD9704 Approved
0.5956 Remote Similarity NPD194 Clinical (unspecified phase)
0.5944 Remote Similarity NPD195 Approved
0.5944 Remote Similarity NPD186 Discovery
0.5929 Remote Similarity NPD1431 Approved
0.5929 Remote Similarity NPD1430 Approved
0.5915 Remote Similarity NPD171 Discontinued
0.5912 Remote Similarity NPD252 Clinical (unspecified phase)
0.5882 Remote Similarity NPD8859 Approved
0.5882 Remote Similarity NPD8861 Approved
0.5882 Remote Similarity NPD209 Clinical (unspecified phase)
0.5882 Remote Similarity NPD8862 Approved
0.587 Remote Similarity NPD9550 Approved
0.587 Remote Similarity NPD9551 Approved
0.5857 Remote Similarity NPD549 Approved
0.5827 Remote Similarity NPD799 Phase 1
0.5811 Remote Similarity NPD3107 Discontinued
0.5811 Remote Similarity NPD1369 Phase 2
0.5811 Remote Similarity NPD1750 Clinical (unspecified phase)
0.5802 Remote Similarity NPD798 Discontinued
0.58 Remote Similarity NPD2646 Discontinued
0.58 Remote Similarity NPD2624 Phase 2
0.5782 Remote Similarity NPD283 Approved
0.5778 Remote Similarity NPD9632 Phase 3
0.5714 Remote Similarity NPD4812 Phase 1
0.5705 Remote Similarity NPD242 Approved
0.5705 Remote Similarity NPD338 Approved
0.5695 Remote Similarity NPD1732 Phase 3
0.5672 Remote Similarity NPD300 Approved
0.5667 Remote Similarity NPD339 Approved
0.5664 Remote Similarity NPD8565 Clinical (unspecified phase)
0.5638 Remote Similarity NPD536 Clinical (unspecified phase)
0.5629 Remote Similarity NPD169 Phase 2
0.5625 Remote Similarity NPD5666 Phase 2
0.56 Remote Similarity NPD213 Clinical (unspecified phase)
0.56 Remote Similarity NPD214 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