Structure

Physi-Chem Properties

Molecular Weight:  146.07
Volume:  138.128
LogP:  -2.268
LogD:  -1.22
LogS:  -0.938
# Rotatable Bonds:  5
TPSA:  92.42
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.467
Synthetic Accessibility Score:  1.877
Fsp3:  0.6
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:  -5.837
MDCK Permeability:  0.0008115764358080924
Pgp-inhibitor:  0.004
Pgp-substrate:  0.759
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.168

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.979
Plasma Protein Binding (PPB):  12.170969009399414%
Volume Distribution (VD):  0.314
Pgp-substrate:  79.6703109741211%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.06
CYP2C19-inhibitor:  0.042
CYP2C19-substrate:  0.051
CYP2C9-inhibitor:  0.019
CYP2C9-substrate:  0.76
CYP2D6-inhibitor:  0.031
CYP2D6-substrate:  0.209
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.02

ADMET: Excretion

Clearance (CL):  5.692
Half-life (T1/2):  0.689

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.05
Drug-inuced Liver Injury (DILI):  0.653
AMES Toxicity:  0.033
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.019
Skin Sensitization:  0.228
Carcinogencity:  0.021
Eye Corrosion:  0.003
Eye Irritation:  0.165
Respiratory Toxicity:  0.018

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

  Natural Product: NPC202525

Natural Product ID:  NPC202525
Common Name*:   4-(Carbamoylamino)Butanoic Acid
IUPAC Name:   4-(carbamoylamino)butanoic acid
Synonyms:   4-Ureido-Butyric Acid
Standard InCHIKey:  QYTWIMMLQKHPGL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H10N2O3/c6-5(10)7-3-1-2-4(8)9/h1-3H2,(H,8,9)(H3,6,7,10)
SMILES:  OC(=O)CCCNC(=N)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL310895
PubChem CID:   1571307
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0001880] Gamma amino acids 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
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. fruit n.a. DOI[10.1016/S0040-4039(01)00209-X]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[10575373]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota Leaves n.a. n.a. PMID[12713396]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. leaf n.a. PMID[15467205]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. whole plant n.a. PMID[16808005]
NPO29090 Carpesium triste Species Asteraceae Eukaryota Seeds n.a. n.a. PMID[17432904]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota roots n.a. n.a. PMID[20022509]
NPO29209 Litchi chinensis Species Sapindaceae Eukaryota n.a. seed n.a. PMID[21287989]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21866899]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[23102654]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[23325115]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota Roots n.a. n.a. PMID[23541646]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[28140583]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[31103896]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[7381508]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28928 Piper nigrum Species Piperaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29231 Prosopis juliflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15111 Ustilaginoidea virens Species n.a. Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29209 Litchi chinensis Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25796 Nekemias chaffanjonii Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15111 Ustilaginoidea virens Species n.a. Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29231 Prosopis juliflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29209 Litchi chinensis Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29209 Litchi chinensis Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29209 Litchi chinensis Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29492 Lolium rigidum Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28790 Pithecellobium cubense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29231 Prosopis juliflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29370 Astragalus angustifolius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29267 Ryparosa acuminata Species Achariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15111 Ustilaginoidea virens Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29209 Litchi chinensis Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29160 Mollugo hirta Species Molluginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29090 Carpesium triste Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25852 Royena zombensis Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28849 Lobularia maritima Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29480 Rapanea maximowiczii Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29178 Hyla arborea Species Hylidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29406 Paralithodes brevipes Species Lithodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29297 Frasera albicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29248 Pseudospiropes simplex n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28956 Ammoides pusilla Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25796 Nekemias chaffanjonii Species Vitaceae 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
NPT64 Individual Protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 25918.5 nM PMID[554503]
NPT805 Protein Complex GABA-A receptor; anion channel Rattus norvegicus Ki = 100000.0 nM PMID[554502]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 18526.0 nM PMID[554503]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 10417.9 nM PMID[554503]
NPT2 Others Unspecified "" Potency n.a. 7943.3 nM PMID[554503]
NPT2 Others Unspecified "" Potency n.a. 35481.3 nM PMID[554503]

☑ 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 NPC202525 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 NPC245768
0.7833 Intermediate Similarity NPC325534
0.7759 Intermediate Similarity NPC118429
0.7636 Intermediate Similarity NPC10915
0.7458 Intermediate Similarity NPC322206
0.7447 Intermediate Similarity NPC18188
0.7213 Intermediate Similarity NPC103130
0.7213 Intermediate Similarity NPC226453
0.7097 Intermediate Similarity NPC278881
0.7031 Intermediate Similarity NPC81647
0.6984 Remote Similarity NPC327985
0.6923 Remote Similarity NPC329263
0.6667 Remote Similarity NPC133183
0.6607 Remote Similarity NPC204607
0.6491 Remote Similarity NPC200550
0.6491 Remote Similarity NPC155156
0.6471 Remote Similarity NPC328457
0.6452 Remote Similarity NPC177191
0.6429 Remote Similarity NPC17244
0.6415 Remote Similarity NPC40511
0.6327 Remote Similarity NPC229838
0.6271 Remote Similarity NPC322091
0.6271 Remote Similarity NPC60672
0.625 Remote Similarity NPC315780
0.625 Remote Similarity NPC327542
0.6226 Remote Similarity NPC276294
0.6182 Remote Similarity NPC195448
0.6154 Remote Similarity NPC121517
0.6154 Remote Similarity NPC326992
0.6154 Remote Similarity NPC168375
0.6154 Remote Similarity NPC66043
0.6111 Remote Similarity NPC198301
0.6111 Remote Similarity NPC323974
0.6102 Remote Similarity NPC190184
0.6102 Remote Similarity NPC197087
0.6066 Remote Similarity NPC38463
0.6066 Remote Similarity NPC325985
0.6034 Remote Similarity NPC137958
0.6034 Remote Similarity NPC273330
0.6 Remote Similarity NPC118459
0.6 Remote Similarity NPC327698
0.5968 Remote Similarity NPC278209
0.5965 Remote Similarity NPC93081
0.5965 Remote Similarity NPC140872
0.5965 Remote Similarity NPC153370
0.5938 Remote Similarity NPC143722
0.5926 Remote Similarity NPC291186
0.5926 Remote Similarity NPC167986
0.5893 Remote Similarity NPC297220
0.589 Remote Similarity NPC122471
0.5873 Remote Similarity NPC245346
0.5873 Remote Similarity NPC11433
0.5873 Remote Similarity NPC302003
0.5862 Remote Similarity NPC324825
0.5862 Remote Similarity NPC112890
0.5862 Remote Similarity NPC316231
0.5862 Remote Similarity NPC328378
0.5846 Remote Similarity NPC273037
0.5818 Remote Similarity NPC132307
0.5818 Remote Similarity NPC325097
0.5818 Remote Similarity NPC126925
0.58 Remote Similarity NPC163099
0.5789 Remote Similarity NPC136159
0.5781 Remote Similarity NPC268927
0.5781 Remote Similarity NPC64250
0.5781 Remote Similarity NPC276928
0.5781 Remote Similarity NPC321536
0.5763 Remote Similarity NPC295832
0.5763 Remote Similarity NPC27359
0.5763 Remote Similarity NPC198398
0.5738 Remote Similarity NPC316889
0.5738 Remote Similarity NPC321118
0.5714 Remote Similarity NPC114517
0.5645 Remote Similarity NPC322573
0.5645 Remote Similarity NPC2801
0.5645 Remote Similarity NPC327831
0.5625 Remote Similarity NPC176164
0.5625 Remote Similarity NPC189301
0.5614 Remote Similarity NPC49952
0.5614 Remote Similarity NPC136476
0.561 Remote Similarity NPC304454

  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 NPC202525 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
0.7833 Intermediate Similarity NPD8952 Approved
0.7759 Intermediate Similarity NPD9014 Approved
0.7447 Intermediate Similarity NPD8623 Phase 1
0.7213 Intermediate Similarity NPD9046 Phase 3
0.7213 Intermediate Similarity NPD9047 Approved
0.7213 Intermediate Similarity NPD9045 Approved
0.7213 Intermediate Similarity NPD9048 Approved
0.697 Remote Similarity NPD5382 Phase 2
0.6875 Remote Similarity NPD9232 Phase 2
0.6875 Remote Similarity NPD9231 Phase 3
0.6875 Remote Similarity NPD9233 Phase 3
0.6769 Remote Similarity NPD9451 Clinical (unspecified phase)
0.6429 Remote Similarity NPD9230 Discontinued
0.6286 Remote Similarity NPD366 Approved
0.6269 Remote Similarity NPD9452 Clinical (unspecified phase)
0.6182 Remote Similarity NPD8621 Approved
0.6111 Remote Similarity NPD9019 Approved
0.6102 Remote Similarity NPD8785 Approved
0.6066 Remote Similarity NPD8864 Clinical (unspecified phase)
0.6066 Remote Similarity NPD8949 Discontinued
0.6034 Remote Similarity NPD8872 Phase 3
0.6034 Remote Similarity NPD8871 Approved
0.6 Remote Similarity NPD9658 Clinical (unspecified phase)
0.5965 Remote Similarity NPD8808 Approved
0.5965 Remote Similarity NPD8809 Approved
0.5965 Remote Similarity NPD8614 Approved
0.5926 Remote Similarity NPD8805 Approved
0.5926 Remote Similarity NPD8804 Approved
0.5893 Remote Similarity NPD8793 Approved
0.5893 Remote Similarity NPD8792 Approved
0.5873 Remote Similarity NPD9433 Approved
0.5873 Remote Similarity NPD8865 Approved
0.5862 Remote Similarity NPD9044 Approved
0.5833 Remote Similarity NPD8851 Phase 1
0.5818 Remote Similarity NPD8798 Approved
0.5763 Remote Similarity NPD9226 Approved
0.5763 Remote Similarity NPD9225 Phase 3
0.5735 Remote Similarity NPD9442 Clinical (unspecified phase)
0.5645 Remote Similarity NPD8971 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