Structure

Physi-Chem Properties

Molecular Weight:  175.1
Volume:  166.42
LogP:  -3.609
LogD:  -1.554
LogS:  -1.378
# Rotatable Bonds:  6
TPSA:  118.44
# H-Bond Aceptor:  6
# H-Bond Donor:  6
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.394
Synthetic Accessibility Score:  2.56
Fsp3:  0.667
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:  -6.132
MDCK Permeability:  0.0025121518410742283
Pgp-inhibitor:  0.004
Pgp-substrate:  0.595
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.754
Plasma Protein Binding (PPB):  6.077785491943359%
Volume Distribution (VD):  0.486
Pgp-substrate:  89.87064361572266%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.032
CYP2C19-inhibitor:  0.053
CYP2C19-substrate:  0.05
CYP2C9-inhibitor:  0.026
CYP2C9-substrate:  0.161
CYP2D6-inhibitor:  0.032
CYP2D6-substrate:  0.208
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.018

ADMET: Excretion

Clearance (CL):  6.925
Half-life (T1/2):  0.482

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.031
Drug-inuced Liver Injury (DILI):  0.036
AMES Toxicity:  0.063
Rat Oral Acute Toxicity:  0.02
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.198
Carcinogencity:  0.019
Eye Corrosion:  0.003
Eye Irritation:  0.04
Respiratory Toxicity:  0.102

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

  Natural Product: NPC118429

Natural Product ID:  NPC118429
Common Name*:   L-Citrulline
IUPAC Name:   (2S)-2-azaniumyl-5-(carbamoylamino)pentanoate
Synonyms:   L-Citrulline
Standard InCHIKey:  RHGKLRLOHDJJDR-BYPYZUCNSA-N
Standard InCHI:  InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12)/t4-/m0/s1
SMILES:  C(C[C@@H](C(=O)O)N)CNC(=N)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL444814
PubChem CID:   6992098
9750
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
NPO22132 NPC118429 Other n.a. 16.57510112 n.a. n.a. mg/100g Database [FooDB]
NPO7576 NPC118429 Other n.a. 5.42 n.a. n.a. mg/100g Database [FooDB]
NPO163 NPC118429 Other n.a. 3.04 n.a. n.a. mg/100g Database [FooDB]
NPO7530 NPC118429 Other n.a. 175.9 n.a. n.a. mg/100g Database [FooDB]
NPO27241 NPC118429 Other n.a. 7.4 n.a. n.a. mg/100g Database [FooDB]
NPO21460 NPC118429 Other n.a. 1.88 n.a. n.a. mg/100g Database [FooDB]
NPO7732 NPC118429 Other n.a. 6.32 n.a. n.a. mg/100g Database [FooDB]
NPO16501 NPC118429 Other n.a. 7.2 n.a. n.a. mg/100g Database [FooDB]
NPO3938 NPC118429 Other n.a. 18.61 n.a. n.a. mg/100g Database [FooDB]
NPO2776 NPC118429 Other n.a. 0.4 n.a. n.a. mg/100g Database [FooDB]
NPO16509 NPC118429 Other n.a. 99.74973913 n.a. n.a. mg/100g Database [FooDB]
NPO23230 NPC118429 Other n.a. 4.8 n.a. n.a. mg/100g Database [FooDB]
NPO16501 NPC118429 Other n.a. 17.21 n.a. n.a. mg/100g Database [FooDB]
NPO13642 NPC118429 Other n.a. 2.319549296 n.a. n.a. mg/100g Database [FooDB]
NPO4359 NPC118429 Other n.a. 41.43 n.a. n.a. mg/100g Database [FooDB]
NPO16501 NPC118429 Other n.a. 13.05701053 n.a. n.a. mg/100g Database [FooDB]
NPO25583 NPC118429 Other n.a. 1 n.a. n.a. mg/100g Database [FooDB]
NPO659 NPC118429 Other n.a. 22.2 n.a. n.a. mg/100g Database [FooDB]
NPO14582 NPC118429 Other n.a. 3.3 n.a. n.a. mg/100g Database [FooDB]
NPO18665 NPC118429 Other n.a. 0.7 n.a. n.a. mg/100g Database [FooDB]
NPO3938 NPC118429 Other n.a. 33.4 n.a. n.a. mg/100g Database [FooDB]
NPO25583 NPC118429 Other n.a. 3.955150115 n.a. n.a. mg/100g Database [FooDB]
NPO19774 NPC118429 Other n.a. 8.158030769 n.a. n.a. mg/100g Database [FooDB]
NPO7576 NPC118429 Other n.a. 1.83 n.a. n.a. mg/100g Database [FooDB]
NPO3938 NPC118429 Other n.a. 3.58 n.a. n.a. mg/100g Database [FooDB]
NPO441 NPC118429 Other n.a. 1.6 n.a. n.a. mg/100g Database [FooDB]
NPO4934 NPC118429 Other n.a. 20.92 n.a. n.a. mg/100g Database [FooDB]
NPO11120 NPC118429 Other n.a. 0.34 n.a. n.a. mg/100g Database [FooDB]
NPO4934 NPC118429 Other n.a. 26.5 n.a. n.a. mg/100g Database [FooDB]
NPO16501 NPC118429 Other n.a. 9.49 n.a. n.a. mg/100g Database [FooDB]
NPO16509 NPC118429 n.a. n.a. 99.75 n.a. n.a. mg/100g Database [FooDB]
NPO22132 NPC118429 n.a. n.a. 16.58 n.a. n.a. mg/100g Database [FooDB]
NPO16501 NPC118429 n.a. n.a. 13.06 n.a. n.a. mg/100g Database [FooDB]
NPO659 NPC118429 n.a. n.a. 9.26 n.a. n.a. mg/100g Database [FooDB]
NPO23230 NPC118429 n.a. n.a. 4.82 n.a. n.a. mg/100g Database [FooDB]
NPO25583 NPC118429 n.a. n.a. 3.96 n.a. n.a. mg/100g Database [FooDB]
NPO13642 NPC118429 n.a. n.a. 2.32 n.a. n.a. mg/100g Database [FooDB]
NPO7530 NPC118429 Raw Fruit 14.6 14.6 14.6 mg/100g Database [DUKE]
NPO13450 NPC118429 Raw Fruit 19.15 14.2 24.1 mg/100g Database [DUKE]

☑ 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
NPT35 Others n.a. Kd = 68000.0 nM PMID[450463]
NPT2 Others Unspecified Inhibition = 0.0 % PMID[450464]
NPT21154 SINGLE PROTEIN General amino-acid permease GAP1 Saccharomyces cerevisiae Km = 37000.0 nM PMID[450465]
NPT73 Individual Protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 135.09 % PMID[450466]
NPT72 Individual Protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 119.67 % PMID[450466]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -3.08 % PMID[450467]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Hit score = 0.1542 n.a. PMID[450468]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 30.93 % PMID[450469]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 17.14 % PMID[450470]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.07 % PMID[450471]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 0.26 % PMID[450472]

☑ 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 NPC118429 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
0.9322 High Similarity NPC226453
0.9322 High Similarity NPC103130
0.9016 High Similarity NPC327985
0.8594 High Similarity NPC133183
0.8333 Intermediate Similarity NPC328457
0.8254 Intermediate Similarity NPC278881
0.8125 Intermediate Similarity NPC325534
0.7857 Intermediate Similarity NPC93081
0.7857 Intermediate Similarity NPC140872
0.7759 Intermediate Similarity NPC202525
0.7667 Intermediate Similarity NPC10915
0.7581 Intermediate Similarity NPC11433
0.7581 Intermediate Similarity NPC245346
0.7581 Intermediate Similarity NPC302003
0.75 Intermediate Similarity NPC322206
0.7333 Intermediate Similarity NPC245768
0.7143 Intermediate Similarity NPC278209
0.7119 Intermediate Similarity NPC112890
0.7119 Intermediate Similarity NPC316231
0.7119 Intermediate Similarity NPC324825
0.7018 Intermediate Similarity NPC118459
0.7018 Intermediate Similarity NPC327698
0.6964 Remote Similarity NPC276294
0.6935 Remote Similarity NPC183845
0.6935 Remote Similarity NPC279661
0.6923 Remote Similarity NPC268927
0.6923 Remote Similarity NPC64250
0.6923 Remote Similarity NPC276928
0.6812 Remote Similarity NPC287693
0.6774 Remote Similarity NPC190184
0.6774 Remote Similarity NPC197087
0.6769 Remote Similarity NPC189301
0.6769 Remote Similarity NPC176164
0.6761 Remote Similarity NPC322274
0.6719 Remote Similarity NPC38463
0.6719 Remote Similarity NPC325985
0.6714 Remote Similarity NPC196359
0.6714 Remote Similarity NPC78312
0.6714 Remote Similarity NPC135539
0.6714 Remote Similarity NPC221764
0.6667 Remote Similarity NPC254541
0.6667 Remote Similarity NPC320598
0.6622 Remote Similarity NPC320221
0.662 Remote Similarity NPC81647
0.6557 Remote Similarity NPC62045
0.6557 Remote Similarity NPC245027
0.6557 Remote Similarity NPC226027
0.6557 Remote Similarity NPC43204
0.6557 Remote Similarity NPC84636
0.6557 Remote Similarity NPC174246
0.6557 Remote Similarity NPC162620
0.6528 Remote Similarity NPC15864
0.65 Remote Similarity NPC101249
0.6494 Remote Similarity NPC191774
0.6452 Remote Similarity NPC137958
0.6452 Remote Similarity NPC273330
0.6441 Remote Similarity NPC329263
0.6418 Remote Similarity NPC321468
0.6418 Remote Similarity NPC321536
0.6418 Remote Similarity NPC317143
0.6418 Remote Similarity NPC316826
0.6418 Remote Similarity NPC327748
0.6406 Remote Similarity NPC60672
0.6406 Remote Similarity NPC322091
0.6364 Remote Similarity NPC317147
0.6364 Remote Similarity NPC318260
0.6324 Remote Similarity NPC327170
0.6324 Remote Similarity NPC143722
0.6324 Remote Similarity NPC329564
0.6316 Remote Similarity NPC327272
0.6316 Remote Similarity NPC121517
0.6316 Remote Similarity NPC168375
0.6316 Remote Similarity NPC326992
0.6308 Remote Similarity NPC322573
0.6271 Remote Similarity NPC323974
0.6271 Remote Similarity NPC198301
0.625 Remote Similarity NPC274499
0.625 Remote Similarity NPC333075
0.625 Remote Similarity NPC8488
0.6164 Remote Similarity NPC107224
0.6129 Remote Similarity NPC153370
0.6102 Remote Similarity NPC291186
0.6102 Remote Similarity NPC167986
0.6094 Remote Similarity NPC155156
0.6094 Remote Similarity NPC200550
0.6087 Remote Similarity NPC177191
0.6087 Remote Similarity NPC68974
0.6066 Remote Similarity NPC297220
0.6061 Remote Similarity NPC2801
0.6056 Remote Similarity NPC289691
0.6032 Remote Similarity NPC328378
0.6024 Remote Similarity NPC199072
0.6 Remote Similarity NPC132307
0.6 Remote Similarity NPC325097
0.6 Remote Similarity NPC126925
0.6 Remote Similarity NPC273037
0.6 Remote Similarity NPC40511
0.5972 Remote Similarity NPC160661
0.5972 Remote Similarity NPC174304
0.5972 Remote Similarity NPC325597
0.5968 Remote Similarity NPC136159
0.5949 Remote Similarity NPC315780
0.5909 Remote Similarity NPC321118
0.5909 Remote Similarity NPC316889
0.5846 Remote Similarity NPC322946
0.5844 Remote Similarity NPC315897
0.5844 Remote Similarity NPC185084
0.5833 Remote Similarity NPC315744
0.5821 Remote Similarity NPC327831
0.5811 Remote Similarity NPC222327
0.5811 Remote Similarity NPC188231
0.5806 Remote Similarity NPC195448
0.5806 Remote Similarity NPC136476
0.5806 Remote Similarity NPC49952
0.5797 Remote Similarity NPC190385
0.5763 Remote Similarity NPC326212
0.5763 Remote Similarity NPC237525
0.5763 Remote Similarity NPC66043
0.5763 Remote Similarity NPC53449
0.5758 Remote Similarity NPC189178
0.5758 Remote Similarity NPC263065
0.5747 Remote Similarity NPC304454
0.5733 Remote Similarity NPC319046
0.5692 Remote Similarity NPC125736
0.5692 Remote Similarity NPC110136
0.5692 Remote Similarity NPC50457
0.569 Remote Similarity NPC18188
0.5658 Remote Similarity NPC126779
0.5645 Remote Similarity NPC208793
0.5645 Remote Similarity NPC285322
0.5618 Remote Similarity NPC304455
0.5614 Remote Similarity NPC116709
0.5614 Remote Similarity NPC272614
0.5614 Remote Similarity NPC21290
0.5606 Remote Similarity NPC19576
0.5606 Remote Similarity NPC155512
0.5606 Remote Similarity NPC29950
0.56 Remote Similarity NPC118524

  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 NPC118429 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
1.0 High Similarity NPD9014 Approved
0.9322 High Similarity NPD9048 Approved
0.9322 High Similarity NPD9047 Approved
0.9322 High Similarity NPD9045 Approved
0.9322 High Similarity NPD9046 Phase 3
0.8871 High Similarity NPD9231 Phase 3
0.8871 High Similarity NPD9232 Phase 2
0.8871 High Similarity NPD9233 Phase 3
0.8125 Intermediate Similarity NPD8952 Approved
0.8088 Intermediate Similarity NPD366 Approved
0.7879 Intermediate Similarity NPD9451 Clinical (unspecified phase)
0.7857 Intermediate Similarity NPD8808 Approved
0.7857 Intermediate Similarity NPD8809 Approved
0.7581 Intermediate Similarity NPD8865 Approved
0.7123 Intermediate Similarity NPD9224 Clinical (unspecified phase)
0.7119 Intermediate Similarity NPD9044 Approved
0.6833 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6774 Remote Similarity NPD8785 Approved
0.6719 Remote Similarity NPD8979 Approved
0.6719 Remote Similarity NPD8981 Clinical (unspecified phase)
0.6719 Remote Similarity NPD8980 Approved
0.6714 Remote Similarity NPD8868 Approved
0.6709 Remote Similarity NPD4829 Discontinued
0.6575 Remote Similarity NPD5382 Phase 2
0.6567 Remote Similarity NPD1155 Discontinued
0.6557 Remote Similarity NPD9018 Approved
0.6557 Remote Similarity NPD9017 Approved
0.6515 Remote Similarity NPD9433 Approved
0.65 Remote Similarity NPD8867 Approved
0.65 Remote Similarity NPD8866 Approved
0.6494 Remote Similarity NPD4278 Clinical (unspecified phase)
0.6452 Remote Similarity NPD8872 Phase 3
0.6452 Remote Similarity NPD8871 Approved
0.6389 Remote Similarity NPD9452 Clinical (unspecified phase)
0.6271 Remote Similarity NPD9019 Approved
0.625 Remote Similarity NPD8851 Phase 1
0.6129 Remote Similarity NPD8614 Approved
0.6102 Remote Similarity NPD8804 Approved
0.6102 Remote Similarity NPD8805 Approved
0.6024 Remote Similarity NPD326 Approved
0.6 Remote Similarity NPD8798 Approved
0.5972 Remote Similarity NPD348 Approved
0.5921 Remote Similarity NPD5386 Phase 2
0.5846 Remote Similarity NPD9441 Phase 2
0.5844 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5811 Remote Similarity NPD1429 Clinical (unspecified phase)
0.5811 Remote Similarity NPD886 Clinical (unspecified phase)
0.5806 Remote Similarity NPD8621 Approved
0.5802 Remote Similarity NPD617 Approved
0.5797 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5789 Remote Similarity NPD2220 Clinical (unspecified phase)
0.5769 Remote Similarity NPD9217 Clinical (unspecified phase)
0.5758 Remote Similarity NPD9204 Approved
0.5758 Remote Similarity NPD9205 Approved
0.5735 Remote Similarity NPD8864 Clinical (unspecified phase)
0.5733 Remote Similarity NPD4241 Registered
0.5733 Remote Similarity NPD337 Discontinued
0.5714 Remote Similarity NPD8973 Approved
0.5714 Remote Similarity NPD8972 Approved
0.5714 Remote Similarity NPD8850 Approved
0.569 Remote Similarity NPD8623 Phase 1
0.5658 Remote Similarity NPD4242 Approved
0.5645 Remote Similarity NPD8610 Approved
0.5641 Remote Similarity NPD6944 Clinical (unspecified phase)
0.5614 Remote Similarity NPD8211 Approved
0.5614 Remote Similarity NPD8210 Phase 3
0.5606 Remote Similarity NPD8847 Approved
0.5606 Remote Similarity NPD61 Approved
0.5606 Remote Similarity NPD8846 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