Structure

Physi-Chem Properties

Molecular Weight:  241.03
Volume:  192.177
LogP:  -2.995
LogD:  -1.71
LogS:  0.02
# Rotatable Bonds:  3
TPSA:  133.16
# H-Bond Aceptor:  8
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.416
Synthetic Accessibility Score:  3.909
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.135
MDCK Permeability:  0.00011333535076119006
Pgp-inhibitor:  0.0
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.924
20% Bioavailability (F20%):  0.999
30% Bioavailability (F30%):  0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.45
Plasma Protein Binding (PPB):  15.624317169189453%
Volume Distribution (VD):  0.305
Pgp-substrate:  83.00032806396484%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.034
CYP2C19-inhibitor:  0.039
CYP2C19-substrate:  0.043
CYP2C9-inhibitor:  0.016
CYP2C9-substrate:  0.683
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.152
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.001

ADMET: Excretion

Clearance (CL):  1.606
Half-life (T1/2):  0.597

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.544
Drug-inuced Liver Injury (DILI):  0.045
AMES Toxicity:  0.651
Rat Oral Acute Toxicity:  0.216
Maximum Recommended Daily Dose:  0.151
Skin Sensitization:  0.693
Carcinogencity:  0.754
Eye Corrosion:  0.035
Eye Irritation:  0.176
Respiratory Toxicity:  0.969

Download Data

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

  Natural Product: NPC219340

Natural Product ID:  NPC219340
Common Name*:   Cribronic Acid
IUPAC Name:   (2S,4R,5R)-5-hydroxy-4-sulfooxypiperidine-2-carboxylic acid
Synonyms:   cribronic acid
Standard InCHIKey:  VGWGHJSLZPTLLA-VPENINKCSA-N
Standard InCHI:  InChI=1S/C6H11NO7S/c8-4-2-7-3(6(9)10)1-5(4)14-15(11,12)13/h3-5,7-8H,1-2H2,(H,9,10)(H,11,12,13)/t3-,4+,5+/m0/s1
SMILES:  C1[C@@H](C(=O)O)NC[C@H]([C@@H]1OS(=O)(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL507082
PubChem CID:   10444353
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
NPO33368 micronesian sponges Species n.a. n.a. n.a. n.a. n.a. PMID[12828462]

☑ 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
NPT32 Organism Mus musculus Mus musculus ED50 = 29.0 pmol PMID[450551]
NPT1496 Protein Complex Glutamate NMDA receptor Rattus norvegicus IC50 = 83.0 nM PMID[450551]

☑ 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 NPC219340 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
0.8919 High Similarity NPC185084
0.8378 Intermediate Similarity NPC107224
0.75 Intermediate Similarity NPC472609
0.7467 Intermediate Similarity NPC306462
0.7467 Intermediate Similarity NPC22774
0.7467 Intermediate Similarity NPC218150
0.7467 Intermediate Similarity NPC150680
0.7467 Intermediate Similarity NPC2432
0.7467 Intermediate Similarity NPC69669
0.7297 Intermediate Similarity NPC276928
0.7297 Intermediate Similarity NPC64250
0.7297 Intermediate Similarity NPC268927
0.7273 Intermediate Similarity NPC75435
0.7273 Intermediate Similarity NPC471892
0.7273 Intermediate Similarity NPC471780
0.7273 Intermediate Similarity NPC142290
0.7273 Intermediate Similarity NPC223386
0.7273 Intermediate Similarity NPC198341
0.72 Intermediate Similarity NPC68974
0.7191 Intermediate Similarity NPC469363
0.7179 Intermediate Similarity NPC286851
0.7179 Intermediate Similarity NPC303798
0.7179 Intermediate Similarity NPC315980
0.7089 Intermediate Similarity NPC221764
0.7089 Intermediate Similarity NPC196359
0.7089 Intermediate Similarity NPC78312
0.7089 Intermediate Similarity NPC135539
0.7067 Intermediate Similarity NPC193593
0.7067 Intermediate Similarity NPC290106
0.7067 Intermediate Similarity NPC143809
0.7067 Intermediate Similarity NPC76726
0.7 Intermediate Similarity NPC471418
0.6923 Remote Similarity NPC106216
0.6923 Remote Similarity NPC88898
0.6914 Remote Similarity NPC268922
0.6747 Remote Similarity NPC28959
0.6747 Remote Similarity NPC476694
0.6747 Remote Similarity NPC476696
0.6747 Remote Similarity NPC255535
0.6747 Remote Similarity NPC476695
0.6747 Remote Similarity NPC299603
0.6747 Remote Similarity NPC137554
0.6747 Remote Similarity NPC285014
0.6711 Remote Similarity NPC204709
0.6623 Remote Similarity NPC170172
0.6548 Remote Similarity NPC306973
0.6404 Remote Similarity NPC98750
0.6341 Remote Similarity NPC69798
0.6341 Remote Similarity NPC473952
0.6341 Remote Similarity NPC77191
0.6341 Remote Similarity NPC101746
0.6341 Remote Similarity NPC116377
0.6333 Remote Similarity NPC70574
0.6296 Remote Similarity NPC163134
0.6296 Remote Similarity NPC471419
0.625 Remote Similarity NPC62507
0.625 Remote Similarity NPC8087
0.622 Remote Similarity NPC160661
0.6207 Remote Similarity NPC208657
0.6196 Remote Similarity NPC271772
0.6196 Remote Similarity NPC36927
0.6139 Remote Similarity NPC160066
0.6092 Remote Similarity NPC55274
0.6076 Remote Similarity NPC190385
0.6076 Remote Similarity NPC245346
0.6076 Remote Similarity NPC302003
0.6076 Remote Similarity NPC11433
0.6049 Remote Similarity NPC30126
0.6049 Remote Similarity NPC57846
0.6049 Remote Similarity NPC474014
0.6047 Remote Similarity NPC473710
0.6047 Remote Similarity NPC475694
0.6024 Remote Similarity NPC474928
0.6 Remote Similarity NPC34291
0.6 Remote Similarity NPC126664
0.5978 Remote Similarity NPC83248
0.5978 Remote Similarity NPC100204
0.5952 Remote Similarity NPC325534
0.5949 Remote Similarity NPC10262
0.5949 Remote Similarity NPC278209
0.5949 Remote Similarity NPC65832
0.5949 Remote Similarity NPC311668
0.593 Remote Similarity NPC15864
0.5909 Remote Similarity NPC474468
0.5882 Remote Similarity NPC322801
0.5882 Remote Similarity NPC291650
0.5882 Remote Similarity NPC129100
0.5867 Remote Similarity NPC324825
0.5867 Remote Similarity NPC112890
0.5867 Remote Similarity NPC316231
0.5802 Remote Similarity NPC471421
0.5802 Remote Similarity NPC233364
0.5789 Remote Similarity NPC273330
0.5789 Remote Similarity NPC165119
0.5789 Remote Similarity NPC137958
0.5776 Remote Similarity NPC477237
0.5773 Remote Similarity NPC83839
0.5769 Remote Similarity NPC183845
0.5769 Remote Similarity NPC279661
0.5761 Remote Similarity NPC37681
0.5696 Remote Similarity NPC2801
0.5679 Remote Similarity NPC93861
0.5679 Remote Similarity NPC112224
0.5679 Remote Similarity NPC327895
0.5679 Remote Similarity NPC43169
0.5678 Remote Similarity NPC477238
0.5647 Remote Similarity NPC233034
0.5647 Remote Similarity NPC278881
0.5625 Remote Similarity NPC325985
0.5612 Remote Similarity NPC90476
0.5612 Remote Similarity NPC69374
0.56 Remote Similarity NPC292345

  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 NPC219340 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
0.7467 Intermediate Similarity NPD9027 Phase 3
0.7467 Intermediate Similarity NPD9029 Phase 3
0.7467 Intermediate Similarity NPD9028 Phase 2
0.7467 Intermediate Similarity NPD9026 Phase 2
0.7089 Intermediate Similarity NPD8868 Approved
0.6538 Remote Similarity NPD9455 Approved
0.6522 Remote Similarity NPD9401 Discovery
0.6456 Remote Similarity NPD393 Approved
0.64 Remote Similarity NPD881 Approved
0.6395 Remote Similarity NPD9217 Clinical (unspecified phase)
0.6329 Remote Similarity NPD9239 Approved
0.6329 Remote Similarity NPD9240 Approved
0.6304 Remote Similarity NPD882 Phase 2
0.6304 Remote Similarity NPD883 Phase 2
0.6207 Remote Similarity NPD67 Phase 2
0.6207 Remote Similarity NPD9034 Approved
0.6092 Remote Similarity NPD6704 Discontinued
0.6076 Remote Similarity NPD9023 Clinical (unspecified phase)
0.6076 Remote Similarity NPD8865 Approved
0.6067 Remote Similarity NPD376 Approved
0.6067 Remote Similarity NPD11 Approved
0.6049 Remote Similarity NPD9022 Phase 2
0.6049 Remote Similarity NPD9024 Phase 2
0.6019 Remote Similarity NPD2255 Approved
0.6 Remote Similarity NPD9443 Clinical (unspecified phase)
0.5977 Remote Similarity NPD9446 Approved
0.5952 Remote Similarity NPD8952 Approved
0.5882 Remote Similarity NPD9031 Approved
0.5882 Remote Similarity NPD9033 Approved
0.5882 Remote Similarity NPD9032 Approved
0.5882 Remote Similarity NPD9030 Approved
0.5867 Remote Similarity NPD9044 Approved
0.5867 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5825 Remote Similarity NPD6428 Approved
0.5794 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5789 Remote Similarity NPD8871 Approved
0.5789 Remote Similarity NPD8872 Phase 3
0.5773 Remote Similarity NPD619 Phase 3
0.5766 Remote Similarity NPD8087 Discontinued
0.5765 Remote Similarity NPD9442 Clinical (unspecified phase)
0.5726 Remote Similarity NPD8346 Approved
0.5726 Remote Similarity NPD8347 Approved
0.5726 Remote Similarity NPD8345 Approved
0.57 Remote Similarity NPD3716 Discontinued
0.5686 Remote Similarity NPD1446 Phase 3
0.5686 Remote Similarity NPD1447 Phase 3
0.5647 Remote Similarity NPD9440 Discontinued
0.5641 Remote Similarity NPD8851 Phase 1
0.5632 Remote Similarity NPD9451 Clinical (unspecified phase)
0.5631 Remote Similarity NPD8394 Approved
0.56 Remote Similarity NPD618 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