Structure

Physi-Chem Properties

Molecular Weight:  193.06
Volume:  171.897
LogP:  -1.941
LogD:  -0.932
LogS:  -2.818
# Rotatable Bonds:  1
TPSA:  118.51
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.446
Synthetic Accessibility Score:  3.28
Fsp3:  0.143
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:  -6.045
MDCK Permeability:  1.2694532415480353e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.184
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.043
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.572
Plasma Protein Binding (PPB):  42.350807189941406%
Volume Distribution (VD):  0.78
Pgp-substrate:  60.90361404418945%

ADMET: Metabolism

CYP1A2-inhibitor:  0.027
CYP1A2-substrate:  0.906
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.035
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.003
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.029
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.209

ADMET: Excretion

Clearance (CL):  5.055
Half-life (T1/2):  0.913

ADMET: Toxicity

hERG Blockers:  0.033
Human Hepatotoxicity (H-HT):  0.99
Drug-inuced Liver Injury (DILI):  0.99
AMES Toxicity:  0.2
Rat Oral Acute Toxicity:  0.268
Maximum Recommended Daily Dose:  0.076
Skin Sensitization:  0.529
Carcinogencity:  0.952
Eye Corrosion:  0.003
Eye Irritation:  0.154
Respiratory Toxicity:  0.982

Download Data

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

  Natural Product: NPC63433

Natural Product ID:  NPC63433
Common Name*:   2-Amino-6-Hydroxymethyl-3H-Pteridin-4-One
IUPAC Name:   2-amino-6-(hydroxymethyl)-1H-pteridin-4-one
Synonyms:  
Standard InCHIKey:  XGWIBNWDLMIPNF-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H7N5O2/c8-7-11-5-4(6(14)12-7)10-3(2-13)1-9-5/h1,13H,2H2,(H3,8,9,11,12,14)
SMILES:  Oc1nc(=N)[nH]c2c1nc(CO)cn2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL101541
PubChem CID:   69736
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000109] Pteridines and derivatives
        • [CHEMONTID:0000110] Pterins 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
NPO31339 Rana nigromaculata, Species Ranidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2602 Usnea longissima Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2602 Usnea longissima Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5178 Pelophylax nigromaculatus Species Ranidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO913 Pelophylax plancyi Species Ranidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30561 Rana nigromaculata Species Ranidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2602 Usnea longissima Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO913 Pelophylax plancyi Species Ranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5178 Pelophylax nigromaculatus Species Ranidae 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
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 180000.0 nM PMID[474923]

☑ 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 NPC63433 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
0.9099 High Similarity NPC240084
0.8417 Intermediate Similarity NPC144223
0.7417 Intermediate Similarity NPC313547
0.7391 Intermediate Similarity NPC59314
0.7258 Intermediate Similarity NPC327579
0.713 Intermediate Similarity NPC293163
0.7049 Intermediate Similarity NPC41958
0.6833 Remote Similarity NPC119133
0.681 Remote Similarity NPC320256
0.6765 Remote Similarity NPC262926
0.672 Remote Similarity NPC327613
0.6715 Remote Similarity NPC61198
0.6583 Remote Similarity NPC273327
0.6573 Remote Similarity NPC89147
0.6573 Remote Similarity NPC274384
0.6529 Remote Similarity NPC10466
0.6529 Remote Similarity NPC317307
0.6496 Remote Similarity NPC324009
0.6496 Remote Similarity NPC9639
0.6479 Remote Similarity NPC186619
0.6449 Remote Similarity NPC319221
0.6389 Remote Similarity NPC211820
0.6389 Remote Similarity NPC318590
0.6389 Remote Similarity NPC251233
0.6377 Remote Similarity NPC57279
0.637 Remote Similarity NPC180462
0.6345 Remote Similarity NPC177169
0.6345 Remote Similarity NPC317746
0.6308 Remote Similarity NPC68938
0.6301 Remote Similarity NPC64705
0.6301 Remote Similarity NPC232408
0.6232 Remote Similarity NPC287876
0.6222 Remote Similarity NPC15566
0.6168 Remote Similarity NPC100312
0.6168 Remote Similarity NPC204104
0.6159 Remote Similarity NPC14330
0.6129 Remote Similarity NPC111132
0.6127 Remote Similarity NPC320818
0.6115 Remote Similarity NPC243319
0.6111 Remote Similarity NPC270637
0.6094 Remote Similarity NPC329046
0.6063 Remote Similarity NPC27699
0.6053 Remote Similarity NPC207633
0.6042 Remote Similarity NPC30326
0.6032 Remote Similarity NPC155498
0.6 Remote Similarity NPC51000
0.5986 Remote Similarity NPC315642
0.5986 Remote Similarity NPC74306
0.5985 Remote Similarity NPC248007
0.5984 Remote Similarity NPC180417
0.5968 Remote Similarity NPC187191
0.5968 Remote Similarity NPC326248
0.592 Remote Similarity NPC476561
0.5912 Remote Similarity NPC109322
0.5906 Remote Similarity NPC163105
0.5887 Remote Similarity NPC246193
0.585 Remote Similarity NPC185903
0.585 Remote Similarity NPC317821
0.5849 Remote Similarity NPC14590
0.5846 Remote Similarity NPC4837
0.5846 Remote Similarity NPC312187
0.5845 Remote Similarity NPC235501
0.5845 Remote Similarity NPC470138
0.5827 Remote Similarity NPC476099
0.5817 Remote Similarity NPC150853
0.58 Remote Similarity NPC174020
0.5798 Remote Similarity NPC290449
0.5794 Remote Similarity NPC75844
0.5782 Remote Similarity NPC129756
0.5766 Remote Similarity NPC139776
0.576 Remote Similarity NPC332382
0.5753 Remote Similarity NPC237812
0.5753 Remote Similarity NPC18223
0.5743 Remote Similarity NPC286696
0.5725 Remote Similarity NPC5707
0.5714 Remote Similarity NPC62151
0.5714 Remote Similarity NPC33996
0.5704 Remote Similarity NPC278549
0.5703 Remote Similarity NPC476562
0.5695 Remote Similarity NPC107374
0.5695 Remote Similarity NPC21448
0.5695 Remote Similarity NPC156461
0.5676 Remote Similarity NPC210947
0.5667 Remote Similarity NPC229974
0.5667 Remote Similarity NPC8590
0.5658 Remote Similarity NPC189068
0.5658 Remote Similarity NPC164665
0.5646 Remote Similarity NPC314646
0.5638 Remote Similarity NPC161659
0.5638 Remote Similarity NPC209525
0.5625 Remote Similarity NPC25465
0.5621 Remote Similarity NPC219313
0.5621 Remote Similarity NPC309832
0.5621 Remote Similarity NPC269827
0.5616 Remote Similarity NPC327941
0.5616 Remote Similarity NPC126634

  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 NPC63433 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
0.7944 Intermediate Similarity NPD9101 Discontinued
0.7692 Intermediate Similarity NPD9375 Discontinued
0.757 Intermediate Similarity NPD8835 Approved
0.7541 Intermediate Similarity NPD307 Approved
0.75 Intermediate Similarity NPD9374 Approved
0.7402 Intermediate Similarity NPD515 Phase 1
0.7391 Intermediate Similarity NPD8837 Clinical (unspecified phase)
0.7339 Intermediate Similarity NPD9409 Discontinued
0.7333 Intermediate Similarity NPD9373 Approved
0.7258 Intermediate Similarity NPD9607 Approved
0.7177 Intermediate Similarity NPD9360 Approved
0.7177 Intermediate Similarity NPD9606 Approved
0.6866 Remote Similarity NPD547 Clinical (unspecified phase)
0.6866 Remote Similarity NPD545 Clinical (unspecified phase)
0.6847 Remote Similarity NPD9102 Approved
0.6847 Remote Similarity NPD9103 Approved
0.6833 Remote Similarity NPD9291 Approved
0.6765 Remote Similarity NPD194 Clinical (unspecified phase)
0.6715 Remote Similarity NPD252 Clinical (unspecified phase)
0.6691 Remote Similarity NPD209 Clinical (unspecified phase)
0.6641 Remote Similarity NPD237 Clinical (unspecified phase)
0.6619 Remote Similarity NPD1808 Phase 1
0.6612 Remote Similarity NPD9626 Clinical (unspecified phase)
0.6535 Remote Similarity NPD757 Phase 3
0.6475 Remote Similarity NPD1121 Approved
0.6475 Remote Similarity NPD1120 Approved
0.6438 Remote Similarity NPD775 Approved
0.6408 Remote Similarity NPD549 Approved
0.6364 Remote Similarity NPD1431 Approved
0.6364 Remote Similarity NPD1430 Approved
0.635 Remote Similarity NPD9632 Phase 3
0.6331 Remote Similarity NPD9083 Clinical (unspecified phase)
0.6304 Remote Similarity NPD9650 Phase 3
0.6299 Remote Similarity NPD9082 Approved
0.625 Remote Similarity NPD9366 Approved
0.6232 Remote Similarity NPD8829 Clinical (unspecified phase)
0.62 Remote Similarity NPD3086 Phase 3
0.6133 Remote Similarity NPD3085 Phase 1
0.6129 Remote Similarity NPD8862 Approved
0.6129 Remote Similarity NPD8859 Approved
0.6129 Remote Similarity NPD8861 Approved
0.6115 Remote Similarity NPD9081 Clinical (unspecified phase)
0.6108 Remote Similarity NPD7245 Approved
0.6108 Remote Similarity NPD7246 Clinical (unspecified phase)
0.6063 Remote Similarity NPD8571 Phase 3
0.6031 Remote Similarity NPD9584 Phase 2
0.6014 Remote Similarity NPD300 Approved
0.6 Remote Similarity NPD8838 Approved
0.5987 Remote Similarity NPD7842 Phase 2
0.5986 Remote Similarity NPD582 Approved
0.5985 Remote Similarity NPD9084 Phase 2
0.5984 Remote Similarity NPD1816 Clinical (unspecified phase)
0.5971 Remote Similarity NPD870 Clinical (unspecified phase)
0.5962 Remote Similarity NPD4074 Clinical (unspecified phase)
0.5948 Remote Similarity NPD536 Clinical (unspecified phase)
0.5942 Remote Similarity NPD9408 Phase 3
0.5906 Remote Similarity NPD9345 Clinical (unspecified phase)
0.5891 Remote Similarity NPD613 Phase 2
0.5887 Remote Similarity NPD248 Discontinued
0.5845 Remote Similarity NPD282 Approved
0.5827 Remote Similarity NPD9195 Approved
0.5827 Remote Similarity NPD281 Approved
0.5821 Remote Similarity NPD1368 Approved
0.582 Remote Similarity NPD9190 Approved
0.5816 Remote Similarity NPD9633 Phase 3
0.5816 Remote Similarity NPD1807 Clinical (unspecified phase)
0.5802 Remote Similarity NPD9412 Discontinued
0.5797 Remote Similarity NPD798 Discontinued
0.5794 Remote Similarity NPD8566 Approved
0.5778 Remote Similarity NPD8824 Phase 3
0.576 Remote Similarity NPD9134 Approved
0.576 Remote Similarity NPD9255 Phase 2
0.576 Remote Similarity NPD9135 Approved
0.5753 Remote Similarity NPD9133 Approved
0.5748 Remote Similarity NPD9629 Approved
0.5745 Remote Similarity NPD1128 Approved
0.5745 Remote Similarity NPD1127 Approved
0.5725 Remote Similarity NPD8830 Phase 3
0.5696 Remote Similarity NPD2604 Approved
0.5695 Remote Similarity NPD249 Approved
0.5695 Remote Similarity NPD250 Approved
0.5693 Remote Similarity NPD9290 Approved
0.5692 Remote Similarity NPD9071 Phase 3
0.568 Remote Similarity NPD9193 Approved
0.568 Remote Similarity NPD9194 Approved
0.5667 Remote Similarity NPD1451 Approved
0.5659 Remote Similarity NPD9196 Phase 2
0.5658 Remote Similarity NPD1730 Discontinued
0.5652 Remote Similarity NPD5768 Phase 2
0.5647 Remote Similarity NPD2523 Phase 2
0.5647 Remote Similarity NPD2526 Phase 2
0.5646 Remote Similarity NPD9628 Approved
0.5634 Remote Similarity NPD1354 Approved
0.5634 Remote Similarity NPD1356 Approved
0.5634 Remote Similarity NPD1355 Clinical (unspecified phase)
0.563 Remote Similarity NPD163 Approved
0.563 Remote Similarity NPD9132 Discontinued
0.5629 Remote Similarity NPD5342 Clinical (unspecified phase)
0.5621 Remote Similarity NPD186 Discovery
0.5621 Remote Similarity NPD195 Approved
0.5605 Remote Similarity NPD214 Approved
0.5605 Remote Similarity NPD213 Clinical (unspecified phase)
0.5605 Remote Similarity NPD1731 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