Structure

Physi-Chem Properties

Molecular Weight:  188.13
Volume:  185.923
LogP:  -3.697
LogD:  -1.143
LogS:  -1.644
# Rotatable Bonds:  7
TPSA:  125.22
# H-Bond Aceptor:  6
# H-Bond Donor:  7
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.209
Synthetic Accessibility Score:  2.71
Fsp3:  0.714
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:  -6.376
MDCK Permeability:  0.002664175583049655
Pgp-inhibitor:  0.001
Pgp-substrate:  0.609
Human Intestinal Absorption (HIA):  0.061
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.262

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.501
Plasma Protein Binding (PPB):  6.263400077819824%
Volume Distribution (VD):  0.626
Pgp-substrate:  90.95378875732422%

ADMET: Metabolism

CYP1A2-inhibitor:  0.006
CYP1A2-substrate:  0.032
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.053
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.292
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.011

ADMET: Excretion

Clearance (CL):  7.659
Half-life (T1/2):  0.636

ADMET: Toxicity

hERG Blockers:  0.079
Human Hepatotoxicity (H-HT):  0.03
Drug-inuced Liver Injury (DILI):  0.01
AMES Toxicity:  0.071
Rat Oral Acute Toxicity:  0.106
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.307
Carcinogencity:  0.057
Eye Corrosion:  0.003
Eye Irritation:  0.027
Respiratory Toxicity:  0.473

Download Data

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

  Natural Product: NPC278881

Natural Product ID:  NPC278881
Common Name*:   L-Homoarginine
IUPAC Name:   (2S)-2-amino-6-(diaminomethylideneamino)hexanoic acid
Synonyms:   L-Homoarginine
Standard InCHIKey:  QUOGESRFPZDMMT-YFKPBYRVSA-N
Standard InCHI:  InChI=1S/C7H16N4O2/c8-5(6(12)13)3-1-2-4-11-7(9)10/h5H,1-4,8H2,(H,12,13)(H4,9,10,11)/t5-/m0/s1
SMILES:  C(CCNC(=N)N)C[C@@H](C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL589752
PubChem CID:   9085
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
                • [CHEMONTID:0004146] L-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

☑ 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
NPT1149 Individual Protein Phospholipase A-2-activating protein Homo sapiens IC50 > 5000.0 nM PMID[487761]
NPT802 Individual Protein Alkaline phosphatase, tissue-nonspecific isozyme Homo sapiens IC50 > 5000.0 nM PMID[487761]
NPT801 Individual Protein Intestinal alkaline phosphatase Homo sapiens IC50 > 5000.0 nM PMID[487761]
NPT317 Uncleic Acid Nucleic Acid Kd = 7000.0 nM PMID[487762]
NPT317 Uncleic Acid Nucleic Acid INH = 27.0 Miller_unit PMID[487762]
NPT2709 Organism Bacillus subtilis subsp. subtilis str. 168 Bacillus subtilis subsp. subtilis str. 168 MIC > 5000000.0 nM PMID[487762]
NPT2 Others Unspecified Kd = 7000.0 nM PMID[487763]

☑ 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 NPC278881 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
0.8871 High Similarity NPC103130
0.8871 High Similarity NPC226453
0.8594 High Similarity NPC327985
0.8485 Intermediate Similarity NPC133183
0.8254 Intermediate Similarity NPC118429
0.8235 Intermediate Similarity NPC328457
0.7903 Intermediate Similarity NPC278209
0.7656 Intermediate Similarity NPC320598
0.7627 Intermediate Similarity NPC316231
0.7627 Intermediate Similarity NPC324825
0.7627 Intermediate Similarity NPC112890
0.7541 Intermediate Similarity NPC245768
0.75 Intermediate Similarity NPC189301
0.75 Intermediate Similarity NPC176164
0.75 Intermediate Similarity NPC325534
0.7385 Intermediate Similarity NPC254541
0.7385 Intermediate Similarity NPC268927
0.7385 Intermediate Similarity NPC276928
0.7385 Intermediate Similarity NPC64250
0.7097 Intermediate Similarity NPC202525
0.7031 Intermediate Similarity NPC10915
0.6912 Remote Similarity NPC322206
0.6885 Remote Similarity NPC93081
0.6885 Remote Similarity NPC140872
0.6883 Remote Similarity NPC191774
0.6875 Remote Similarity NPC279661
0.6875 Remote Similarity NPC183845
0.678 Remote Similarity NPC323974
0.6716 Remote Similarity NPC11433
0.6716 Remote Similarity NPC302003
0.6716 Remote Similarity NPC245346
0.6667 Remote Similarity NPC118459
0.6667 Remote Similarity NPC304454
0.6667 Remote Similarity NPC327698
0.6618 Remote Similarity NPC321536
0.6575 Remote Similarity NPC107224
0.6522 Remote Similarity NPC68974
0.6486 Remote Similarity NPC15864
0.6479 Remote Similarity NPC315744
0.6462 Remote Similarity NPC197087
0.6462 Remote Similarity NPC190184
0.6418 Remote Similarity NPC38463
0.6418 Remote Similarity NPC325985
0.6406 Remote Similarity NPC50457
0.6386 Remote Similarity NPC199072
0.6377 Remote Similarity NPC316826
0.6377 Remote Similarity NPC327748
0.6377 Remote Similarity NPC317143
0.6377 Remote Similarity NPC321468
0.6364 Remote Similarity NPC60672
0.6364 Remote Similarity NPC322091
0.6351 Remote Similarity NPC81647
0.6324 Remote Similarity NPC317147
0.6324 Remote Similarity NPC318260
0.6286 Remote Similarity NPC329564
0.6286 Remote Similarity NPC327170
0.6286 Remote Similarity NPC143722
0.625 Remote Similarity NPC226027
0.625 Remote Similarity NPC174246
0.625 Remote Similarity NPC84636
0.625 Remote Similarity NPC245027
0.625 Remote Similarity NPC162620
0.625 Remote Similarity NPC43204
0.625 Remote Similarity NPC62045
0.6234 Remote Similarity NPC185084
0.6234 Remote Similarity NPC315897
0.623 Remote Similarity NPC40511
0.6154 Remote Similarity NPC137958
0.6154 Remote Similarity NPC273330
0.6136 Remote Similarity NPC304455
0.6129 Remote Similarity NPC329263
0.6066 Remote Similarity NPC276294
0.6061 Remote Similarity NPC155512
0.6056 Remote Similarity NPC177191
0.6032 Remote Similarity NPC195448
0.6029 Remote Similarity NPC322573
0.6027 Remote Similarity NPC57420
0.6 Remote Similarity NPC78312
0.6 Remote Similarity NPC135539
0.6 Remote Similarity NPC121517
0.6 Remote Similarity NPC221764
0.6 Remote Similarity NPC196359
0.6 Remote Similarity NPC168375
0.6 Remote Similarity NPC326992
0.5968 Remote Similarity NPC198301
0.5949 Remote Similarity NPC320221
0.5946 Remote Similarity NPC174304
0.5946 Remote Similarity NPC325597
0.5932 Remote Similarity NPC270319
0.5921 Remote Similarity NPC319046
0.5882 Remote Similarity NPC321118
0.5882 Remote Similarity NPC316889
0.5867 Remote Similarity NPC287693
0.5846 Remote Similarity NPC153370
0.5844 Remote Similarity NPC126779
0.5844 Remote Similarity NPC322274
0.5823 Remote Similarity NPC55274
0.5821 Remote Similarity NPC200550
0.5821 Remote Similarity NPC155156
0.5811 Remote Similarity NPC289691
0.5806 Remote Similarity NPC167986
0.5806 Remote Similarity NPC291186
0.5797 Remote Similarity NPC2801
0.5789 Remote Similarity NPC314221
0.5789 Remote Similarity NPC222327
0.5789 Remote Similarity NPC188231
0.5789 Remote Similarity NPC60424
0.5781 Remote Similarity NPC297220
0.5758 Remote Similarity NPC328378
0.5753 Remote Similarity NPC273037
0.5745 Remote Similarity NPC3604
0.5745 Remote Similarity NPC471257
0.5733 Remote Similarity NPC472609
0.5732 Remote Similarity NPC315780
0.5714 Remote Similarity NPC126925
0.5714 Remote Similarity NPC325097
0.5714 Remote Similarity NPC132307
0.5696 Remote Similarity NPC306973
0.5692 Remote Similarity NPC101249
0.5692 Remote Similarity NPC136159
0.5684 Remote Similarity NPC472736
0.5682 Remote Similarity NPC469363
0.5679 Remote Similarity NPC327272
0.5672 Remote Similarity NPC110136
0.5672 Remote Similarity NPC125736
0.5647 Remote Similarity NPC219340
0.5612 Remote Similarity NPC471258

  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 NPC278881 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
0.8871 High Similarity NPD9047 Approved
0.8871 High Similarity NPD9046 Phase 3
0.8871 High Similarity NPD9045 Approved
0.8871 High Similarity NPD9048 Approved
0.875 High Similarity NPD9233 Phase 3
0.875 High Similarity NPD9232 Phase 2
0.875 High Similarity NPD9231 Phase 3
0.8615 High Similarity NPD9451 Clinical (unspecified phase)
0.8254 Intermediate Similarity NPD9014 Approved
0.8 Intermediate Similarity NPD366 Approved
0.7627 Intermediate Similarity NPD9044 Approved
0.75 Intermediate Similarity NPD8952 Approved
0.7333 Intermediate Similarity NPD9016 Clinical (unspecified phase)
0.7308 Intermediate Similarity NPD4829 Discontinued
0.6885 Remote Similarity NPD8808 Approved
0.6885 Remote Similarity NPD8809 Approved
0.6883 Remote Similarity NPD4278 Clinical (unspecified phase)
0.6842 Remote Similarity NPD9224 Clinical (unspecified phase)
0.678 Remote Similarity NPD9019 Approved
0.6765 Remote Similarity NPD1155 Discontinued
0.6716 Remote Similarity NPD8865 Approved
0.6533 Remote Similarity NPD5382 Phase 2
0.6484 Remote Similarity NPD4825 Clinical (unspecified phase)
0.6462 Remote Similarity NPD8785 Approved
0.6447 Remote Similarity NPD6944 Clinical (unspecified phase)
0.6386 Remote Similarity NPD326 Approved
0.6351 Remote Similarity NPD9452 Clinical (unspecified phase)
0.625 Remote Similarity NPD9017 Approved
0.625 Remote Similarity NPD9018 Approved
0.6234 Remote Similarity NPD1825 Clinical (unspecified phase)
0.6232 Remote Similarity NPD9433 Approved
0.6184 Remote Similarity NPD2702 Phase 1
0.6184 Remote Similarity NPD2704 Phase 3
0.6154 Remote Similarity NPD8872 Phase 3
0.6154 Remote Similarity NPD8871 Approved
0.6154 Remote Similarity NPD9217 Clinical (unspecified phase)
0.6104 Remote Similarity NPD5386 Phase 2
0.6032 Remote Similarity NPD8621 Approved
0.6 Remote Similarity NPD1429 Clinical (unspecified phase)
0.6 Remote Similarity NPD8868 Approved
0.5976 Remote Similarity NPD617 Approved
0.597 Remote Similarity NPD8851 Phase 1
0.5946 Remote Similarity NPD348 Approved
0.5942 Remote Similarity NPD9454 Approved
0.5942 Remote Similarity NPD8979 Approved
0.5942 Remote Similarity NPD8980 Approved
0.5942 Remote Similarity NPD8981 Clinical (unspecified phase)
0.5942 Remote Similarity NPD8864 Clinical (unspecified phase)
0.5921 Remote Similarity NPD337 Discontinued
0.5921 Remote Similarity NPD4241 Registered
0.589 Remote Similarity NPD9676 Phase 3
0.5846 Remote Similarity NPD8614 Approved
0.5844 Remote Similarity NPD4242 Approved
0.5844 Remote Similarity NPD3213 Discontinued
0.5806 Remote Similarity NPD9458 Approved
0.5806 Remote Similarity NPD8805 Approved
0.5806 Remote Similarity NPD8804 Approved
0.5789 Remote Similarity NPD9421 Phase 1
0.5789 Remote Similarity NPD886 Clinical (unspecified phase)
0.5729 Remote Similarity NPD6120 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8798 Approved
0.57 Remote Similarity NPD1828 Approved
0.57 Remote Similarity NPD1829 Clinical (unspecified phase)
0.57 Remote Similarity NPD1827 Clinical (unspecified phase)
0.5696 Remote Similarity NPD2262 Clinical (unspecified phase)
0.5692 Remote Similarity NPD8866 Approved
0.5692 Remote Similarity NPD8867 Approved
0.5658 Remote Similarity NPD2703 Discontinued
0.5625 Remote Similarity NPD1147 Phase 2

  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