Structure

Physi-Chem Properties

Molecular Weight:  258.01
Volume:  205.999
LogP:  -2.368
LogD:  -2.204
LogS:  -0.154
# Rotatable Bonds:  7
TPSA:  158.43
# H-Bond Aceptor:  9
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.219
Synthetic Accessibility Score:  5.035
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.042
MDCK Permeability:  0.0030129586812108755
Pgp-inhibitor:  0.002
Pgp-substrate:  0.974
Human Intestinal Absorption (HIA):  0.288
20% Bioavailability (F20%):  0.915
30% Bioavailability (F30%):  0.901

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.691
Plasma Protein Binding (PPB):  19.231365203857422%
Volume Distribution (VD):  0.292
Pgp-substrate:  82.77975463867188%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.037
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.039
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.381
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.099
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.006

ADMET: Excretion

Clearance (CL):  1.535
Half-life (T1/2):  0.954

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.051
Drug-inuced Liver Injury (DILI):  0.516
AMES Toxicity:  0.083
Rat Oral Acute Toxicity:  0.011
Maximum Recommended Daily Dose:  0.103
Skin Sensitization:  0.725
Carcinogencity:  0.03
Eye Corrosion:  0.043
Eye Irritation:  0.804
Respiratory Toxicity:  0.826

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  Natural Product: NPC320296

Natural Product ID:  NPC320296
Common Name*:   2-Keto-3-Deoxy-6-Phosphogluconate
IUPAC Name:   (4S,5R)-4,5-dihydroxy-2-oxo-6-phosphonooxyhexanoic acid
Synonyms:  
Standard InCHIKey:  OVPRPPOVAXRCED-WVZVXSGGSA-N
Standard InCHI:  InChI=1S/C6H11O9P/c7-3(1-4(8)6(10)11)5(9)2-15-16(12,13)14/h3,5,7,9H,1-2H2,(H,10,11)(H2,12,13,14)/t3-,5+/m0/s1
SMILES:  O[C@H]([C@@H](COP(=O)(O)O)O)CC(=O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1162150
PubChem CID:   3080745
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000389] Keto acids and derivatives
        • [CHEMONTID:0001415] Medium-chain keto 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
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1016/0006-291X(79)91731-5]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1093/emboj/18.8.2021]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1091286]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[10977898]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1100617]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11745165]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11750815]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12369847]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12467448]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12805358]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. ChEBI[131529]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13610867]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13831814]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[14973046]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15031653]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15292242]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15610037]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1644759]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[16630633]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[170247]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[17765195]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[179975]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19026742]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19514719]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19561621]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21437340]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21988831]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22289691]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22855027]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23537328]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23676670]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[241475]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24206068]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24783849]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24831709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24939187]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24966042]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24967680]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[2543976]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[25867074]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26195826]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26337258]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26670289]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26826371]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[29897754]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[30302998]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[318639]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[3283102]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[398096]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4877125]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4879561]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4908789]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[5332408]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6102982]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6284709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6338507]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7042909]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7601837]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[8852895]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[9470222]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria 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
NPT24795 SINGLE PROTEIN KHG/KDPG aldolase Escherichia coli (strain K12) Kcat = 0.3 mM PMID[468314]
NPT2 Others Unspecified Ratio = 800.0 /mM/s PMID[468314]
NPT24795 SINGLE PROTEIN KHG/KDPG aldolase Escherichia coli (strain K12) Kcat = 0.02 /s PMID[468314]
NPT2 Others Unspecified Kcat = 80.0 /s PMID[468314]
NPT2 Others Unspecified Km = 0.1 /s PMID[468314]
NPT24795 SINGLE PROTEIN KHG/KDPG aldolase Escherichia coli (strain K12) Kcat = 9.8 /s PMID[468314]
NPT24795 SINGLE PROTEIN KHG/KDPG aldolase Escherichia coli (strain K12) Km = 200000.0 nM PMID[468314]
NPT24795 SINGLE PROTEIN KHG/KDPG aldolase Escherichia coli (strain K12) Ratio = 0.07 /mM/s PMID[468314]
NPT24795 SINGLE PROTEIN KHG/KDPG aldolase Escherichia coli (strain K12) Ratio = 58.0 /mM/s PMID[468314]
NPT2 Others Unspecified Kcat = 0.1 /s PMID[468314]
NPT2 Others Unspecified Km = 1300000.0 nM PMID[468314]
NPT24796 SINGLE PROTEIN 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Escherichia coli (strain K12) Kcat = 0.01 /s PMID[468314]
NPT24796 SINGLE PROTEIN 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Escherichia coli (strain K12) Km = 90000.0 nM PMID[468314]
NPT24796 SINGLE PROTEIN 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Escherichia coli (strain K12) Kcat = 0.007 /s PMID[468314]
NPT24796 SINGLE PROTEIN 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Escherichia coli (strain K12) Km = 500000.0 nM PMID[468314]
NPT2 Others Unspecified Ratio = 0.1 /mM/s PMID[468314]
NPT24796 SINGLE PROTEIN 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Escherichia coli (strain K12) Ratio = 0.1 /mM/s PMID[468314]
NPT24796 SINGLE PROTEIN 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Escherichia coli (strain K12) Ratio = 0.02 /mM/s PMID[468314]

☑ 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 NPC320296 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
0.9821 High Similarity NPC323945
0.8947 High Similarity NPC3547
0.875 High Similarity NPC196612
0.8571 High Similarity NPC277878
0.8036 Intermediate Similarity NPC328954
0.7869 Intermediate Similarity NPC220922
0.7869 Intermediate Similarity NPC293692
0.7857 Intermediate Similarity NPC172086
0.7857 Intermediate Similarity NPC247546
0.7273 Intermediate Similarity NPC317651
0.7273 Intermediate Similarity NPC258690
0.7101 Intermediate Similarity NPC32148
0.7097 Intermediate Similarity NPC6883
0.7018 Intermediate Similarity NPC242655
0.7018 Intermediate Similarity NPC38891
0.6964 Remote Similarity NPC228782
0.6964 Remote Similarity NPC313565
0.6964 Remote Similarity NPC259982
0.6935 Remote Similarity NPC19676
0.6935 Remote Similarity NPC323401
0.6842 Remote Similarity NPC320624
0.6842 Remote Similarity NPC318951
0.6786 Remote Similarity NPC35661
0.6786 Remote Similarity NPC325307
0.6786 Remote Similarity NPC322956
0.6774 Remote Similarity NPC317680
0.6724 Remote Similarity NPC270088
0.6575 Remote Similarity NPC321873
0.6557 Remote Similarity NPC46254
0.6491 Remote Similarity NPC100742
0.6491 Remote Similarity NPC121018
0.6491 Remote Similarity NPC192402
0.6491 Remote Similarity NPC24751
0.6491 Remote Similarity NPC97444
0.6491 Remote Similarity NPC19044
0.6389 Remote Similarity NPC53879
0.6389 Remote Similarity NPC57788
0.6349 Remote Similarity NPC329095
0.6324 Remote Similarity NPC17935
0.6316 Remote Similarity NPC320331
0.629 Remote Similarity NPC325822
0.629 Remote Similarity NPC61270
0.629 Remote Similarity NPC293378
0.625 Remote Similarity NPC103672
0.625 Remote Similarity NPC320043
0.6154 Remote Similarity NPC317626
0.6154 Remote Similarity NPC317501
0.6154 Remote Similarity NPC65985
0.6154 Remote Similarity NPC314821
0.6145 Remote Similarity NPC316819
0.6119 Remote Similarity NPC198377
0.6056 Remote Similarity NPC268243
0.6029 Remote Similarity NPC61567
0.6 Remote Similarity NPC321102
0.6 Remote Similarity NPC325153
0.6 Remote Similarity NPC278465
0.6 Remote Similarity NPC322803
0.597 Remote Similarity NPC60830
0.597 Remote Similarity NPC68743
0.5968 Remote Similarity NPC314613
0.5955 Remote Similarity NPC327620
0.5942 Remote Similarity NPC179624
0.5921 Remote Similarity NPC470268
0.5897 Remote Similarity NPC125164
0.5873 Remote Similarity NPC200618
0.5873 Remote Similarity NPC131770
0.5802 Remote Similarity NPC317263
0.5789 Remote Similarity NPC109026
0.5738 Remote Similarity NPC319680
0.5714 Remote Similarity NPC320032
0.5714 Remote Similarity NPC86412
0.5714 Remote Similarity NPC192065
0.5714 Remote Similarity NPC293908
0.5714 Remote Similarity NPC322855
0.5714 Remote Similarity NPC317203
0.5714 Remote Similarity NPC66052
0.5714 Remote Similarity NPC325034
0.5692 Remote Similarity NPC90904
0.5692 Remote Similarity NPC322158
0.5692 Remote Similarity NPC329128
0.569 Remote Similarity NPC328950
0.569 Remote Similarity NPC128713
0.5679 Remote Similarity NPC474003
0.5676 Remote Similarity NPC12040
0.5676 Remote Similarity NPC76881
0.5616 Remote Similarity NPC325773
0.5614 Remote Similarity NPC5505
0.5614 Remote Similarity NPC159089
0.5606 Remote Similarity NPC100096
0.56 Remote Similarity NPC241949

  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 NPC320296 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
0.8571 High Similarity NPD65 Approved
0.8571 High Similarity NPD64 Approved
0.8571 High Similarity NPD9008 Approved
0.8571 High Similarity NPD66 Approved
0.8571 High Similarity NPD9007 Approved
0.8571 High Similarity NPD9010 Approved
0.8571 High Similarity NPD9011 Approved
0.8571 High Similarity NPD8960 Approved
0.8571 High Similarity NPD72 Approved
0.8571 High Similarity NPD9009 Approved
0.8305 Intermediate Similarity NPD73 Approved
0.7869 Intermediate Similarity NPD8959 Approved
0.7857 Intermediate Similarity NPD9004 Approved
0.7857 Intermediate Similarity NPD9003 Clinical (unspecified phase)
0.7857 Intermediate Similarity NPD9005 Phase 3
0.7759 Intermediate Similarity NPD9002 Approved
0.7759 Intermediate Similarity NPD9001 Clinical (unspecified phase)
0.7273 Intermediate Similarity NPD8961 Approved
0.7101 Intermediate Similarity NPD898 Approved
0.7101 Intermediate Similarity NPD896 Approved
0.7101 Intermediate Similarity NPD897 Approved
0.6833 Remote Similarity NPD8964 Approved
0.6491 Remote Similarity NPD8598 Approved
0.6491 Remote Similarity NPD8601 Approved
0.6491 Remote Similarity NPD8599 Approved
0.6491 Remote Similarity NPD8605 Approved
0.6491 Remote Similarity NPD8603 Approved
0.6491 Remote Similarity NPD8602 Approved
0.6491 Remote Similarity NPD8604 Approved
0.6491 Remote Similarity NPD8600 Approved
0.6447 Remote Similarity NPD376 Approved
0.6447 Remote Similarity NPD11 Approved
0.629 Remote Similarity NPD9129 Approved
0.629 Remote Similarity NPD9061 Clinical (unspecified phase)
0.629 Remote Similarity NPD9126 Approved
0.629 Remote Similarity NPD71 Approved
0.625 Remote Similarity NPD9049 Discontinued
0.625 Remote Similarity NPD9050 Approved
0.6184 Remote Similarity NPD3181 Approved
0.6154 Remote Similarity NPD9036 Phase 3
0.6154 Remote Similarity NPD9035 Clinical (unspecified phase)
0.6129 Remote Similarity NPD9121 Approved
0.6129 Remote Similarity NPD9122 Approved
0.6129 Remote Similarity NPD9123 Approved
0.6129 Remote Similarity NPD9124 Approved
0.6129 Remote Similarity NPD9127 Approved
0.6129 Remote Similarity NPD108 Approved
0.6129 Remote Similarity NPD9125 Approved
0.6129 Remote Similarity NPD9128 Approved
0.6129 Remote Similarity NPD9130 Phase 3
0.6129 Remote Similarity NPD109 Approved
0.6129 Remote Similarity NPD70 Approved
0.6125 Remote Similarity NPD7329 Approved
0.5882 Remote Similarity NPD619 Phase 3
0.5714 Remote Similarity NPD9052 Approved
0.5714 Remote Similarity NPD9053 Approved
0.5714 Remote Similarity NPD9051 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