Structure

Physi-Chem Properties

Molecular Weight:  147.06
Volume:  131.828
LogP:  -3.548
LogD:  -1.534
LogS:  -1.429
# Rotatable Bonds:  4
TPSA:  118.44
# H-Bond Aceptor:  6
# H-Bond Donor:  6
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.371
Synthetic Accessibility Score:  2.786
Fsp3:  0.5
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:  -6.343
MDCK Permeability:  0.0031332189682871103
Pgp-inhibitor:  0.001
Pgp-substrate:  0.855
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.685
Plasma Protein Binding (PPB):  6.619020938873291%
Volume Distribution (VD):  0.447
Pgp-substrate:  89.28297424316406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.025
CYP2C19-inhibitor:  0.061
CYP2C19-substrate:  0.047
CYP2C9-inhibitor:  0.048
CYP2C9-substrate:  0.14
CYP2D6-inhibitor:  0.023
CYP2D6-substrate:  0.214
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.012

ADMET: Excretion

Clearance (CL):  6.093
Half-life (T1/2):  0.496

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.032
Drug-inuced Liver Injury (DILI):  0.019
AMES Toxicity:  0.153
Rat Oral Acute Toxicity:  0.021
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.179
Carcinogencity:  0.024
Eye Corrosion:  0.003
Eye Irritation:  0.05
Respiratory Toxicity:  0.161

Download Data

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

  Natural Product: NPC10915

Natural Product ID:  NPC10915
Common Name*:   Albizziine
IUPAC Name:   2-amino-3-(carbamoylamino)propanoic acid
Synonyms:  
Standard InCHIKey:  GZYFIMLSHBLMKF-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H9N3O3/c5-2(3(8)9)1-7-4(6)10/h2H,1,5H2,(H,8,9)(H3,6,7,10)
SMILES:  OC(=N)NCC(C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1330613
PubChem CID:   348153
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:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002404] Alpha amino acids

*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
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. bark n.a. PMID[15283458]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. stem n.a. PMID[15577257]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9051910]
NPO31171 Albizzia julibrissin n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO5867 Albizzia lophantha n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5867 Albizzia lophantha n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5867 Albizzia lophantha n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12181 Albizia julibrissin Species Fabaceae 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
NPT282 Individual Protein MAP kinase ERK2 Homo sapiens Potency = 63.1 nM PMID[451077]
NPT73 Individual Protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 118.1 % PMID[451078]
NPT72 Individual Protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 110.81 % PMID[451078]

☑ 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 NPC10915 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
0.8276 Intermediate Similarity NPC322206
0.7667 Intermediate Similarity NPC273037
0.7667 Intermediate Similarity NPC118429
0.7636 Intermediate Similarity NPC202525
0.74 Intermediate Similarity NPC326212
0.74 Intermediate Similarity NPC237525
0.7193 Intermediate Similarity NPC245768
0.7188 Intermediate Similarity NPC325534
0.7143 Intermediate Similarity NPC226453
0.7143 Intermediate Similarity NPC103130
0.7031 Intermediate Similarity NPC278881
0.6981 Remote Similarity NPC198301
0.6923 Remote Similarity NPC327985
0.678 Remote Similarity NPC60672
0.678 Remote Similarity NPC322091
0.6727 Remote Similarity NPC297220
0.6667 Remote Similarity NPC40511
0.6618 Remote Similarity NPC133183
0.6491 Remote Similarity NPC153370
0.6471 Remote Similarity NPC81647
0.6429 Remote Similarity NPC195448
0.6429 Remote Similarity NPC328457
0.6415 Remote Similarity NPC66043
0.6415 Remote Similarity NPC326992
0.6415 Remote Similarity NPC168375
0.6415 Remote Similarity NPC121517
0.6415 Remote Similarity NPC53449
0.6393 Remote Similarity NPC327831
0.6379 Remote Similarity NPC17244
0.6316 Remote Similarity NPC316168
0.6316 Remote Similarity NPC136159
0.6275 Remote Similarity NPC21290
0.6275 Remote Similarity NPC116709
0.6275 Remote Similarity NPC272614
0.625 Remote Similarity NPC208793
0.625 Remote Similarity NPC285322
0.625 Remote Similarity NPC329263
0.6182 Remote Similarity NPC167986
0.6182 Remote Similarity NPC291186
0.6154 Remote Similarity NPC63621
0.614 Remote Similarity NPC185755
0.614 Remote Similarity NPC213876
0.6102 Remote Similarity NPC328378
0.6071 Remote Similarity NPC325097
0.6071 Remote Similarity NPC132307
0.6071 Remote Similarity NPC126925
0.6066 Remote Similarity NPC329495
0.6034 Remote Similarity NPC181588
0.6 Remote Similarity NPC114517
0.6 Remote Similarity NPC319175
0.5968 Remote Similarity NPC321118
0.5968 Remote Similarity NPC316889
0.5965 Remote Similarity NPC118459
0.5965 Remote Similarity NPC327698
0.5946 Remote Similarity NPC192521
0.5942 Remote Similarity NPC193559
0.5938 Remote Similarity NPC278209
0.5932 Remote Similarity NPC140872
0.5932 Remote Similarity NPC93081
0.5909 Remote Similarity NPC177191
0.5902 Remote Similarity NPC200550
0.5902 Remote Similarity NPC155156
0.5862 Remote Similarity NPC49952
0.5862 Remote Similarity NPC309658
0.5862 Remote Similarity NPC136476
0.5849 Remote Similarity NPC69179
0.5846 Remote Similarity NPC245346
0.5846 Remote Similarity NPC11433
0.5846 Remote Similarity NPC302003
0.5833 Remote Similarity NPC112890
0.5833 Remote Similarity NPC316231
0.5833 Remote Similarity NPC324825
0.5806 Remote Similarity NPC197087
0.5806 Remote Similarity NPC190184
0.5789 Remote Similarity NPC315780
0.5781 Remote Similarity NPC38463
0.5781 Remote Similarity NPC325985
0.5763 Remote Similarity NPC204364
0.5758 Remote Similarity NPC276928
0.5758 Remote Similarity NPC268927
0.5758 Remote Similarity NPC64250
0.5738 Remote Similarity NPC114990
0.5738 Remote Similarity NPC125736
0.5714 Remote Similarity NPC326808
0.5714 Remote Similarity NPC226265
0.5714 Remote Similarity NPC254482
0.5714 Remote Similarity NPC219143
0.5714 Remote Similarity NPC317691
0.5714 Remote Similarity NPC110533
0.5692 Remote Similarity NPC283786
0.5676 Remote Similarity NPC126293
0.5667 Remote Similarity NPC227850
0.566 Remote Similarity NPC9294
0.5606 Remote Similarity NPC189301
0.5606 Remote Similarity NPC176164

  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 NPC10915 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
0.7667 Intermediate Similarity NPD9014 Approved
0.7188 Intermediate Similarity NPD8952 Approved
0.7143 Intermediate Similarity NPD9047 Approved
0.7143 Intermediate Similarity NPD9048 Approved
0.7143 Intermediate Similarity NPD9046 Phase 3
0.7143 Intermediate Similarity NPD9045 Approved
0.6912 Remote Similarity NPD5382 Phase 2
0.6833 Remote Similarity NPD8864 Clinical (unspecified phase)
0.6818 Remote Similarity NPD9231 Phase 3
0.6818 Remote Similarity NPD9233 Phase 3
0.6818 Remote Similarity NPD9232 Phase 2
0.6716 Remote Similarity NPD9451 Clinical (unspecified phase)
0.6491 Remote Similarity NPD8614 Approved
0.6471 Remote Similarity NPD9452 Clinical (unspecified phase)
0.6429 Remote Similarity NPD8621 Approved
0.6379 Remote Similarity NPD9230 Discontinued
0.6316 Remote Similarity NPD8208 Clinical (unspecified phase)
0.6316 Remote Similarity NPD8209 Phase 2
0.629 Remote Similarity NPD8949 Discontinued
0.6275 Remote Similarity NPD8211 Approved
0.6275 Remote Similarity NPD8210 Phase 3
0.625 Remote Similarity NPD366 Approved
0.625 Remote Similarity NPD8610 Approved
0.6182 Remote Similarity NPD8804 Approved
0.6182 Remote Similarity NPD8805 Approved
0.614 Remote Similarity NPD8982 Approved
0.6071 Remote Similarity NPD8798 Approved
0.6034 Remote Similarity NPD8810 Clinical (unspecified phase)
0.5949 Remote Similarity NPD4829 Discontinued
0.5932 Remote Similarity NPD8809 Approved
0.5932 Remote Similarity NPD8808 Approved
0.589 Remote Similarity NPD9432 Discontinued
0.5862 Remote Similarity NPD8792 Approved
0.5862 Remote Similarity NPD8793 Approved
0.5846 Remote Similarity NPD8865 Approved
0.5833 Remote Similarity NPD9044 Approved
0.5806 Remote Similarity NPD8785 Approved
0.5763 Remote Similarity NPD399 Approved
0.5763 Remote Similarity NPD400 Approved
0.5763 Remote Similarity NPD398 Approved
0.5714 Remote Similarity NPD8217 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8216 Approved
0.5714 Remote Similarity NPD8215 Approved
0.5714 Remote Similarity NPD8214 Approved
0.5714 Remote Similarity NPD8609 Approved
0.5714 Remote Similarity NPD8545 Approved
0.5676 Remote Similarity NPD9354 Clinical (unspecified phase)
0.5676 Remote Similarity NPD9355 Approved
0.5667 Remote Similarity NPD8873 Approved
0.5606 Remote Similarity NPD9433 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