Structure

Physi-Chem Properties

Molecular Weight:  122.06
Volume:  112.901
LogP:  -1.903
LogD:  -2.088
LogS:  0.356
# Rotatable Bonds:  3
TPSA:  80.92
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.339
Synthetic Accessibility Score:  3.249
Fsp3:  1.0
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:  -5.14
MDCK Permeability:  0.005573571193963289
Pgp-inhibitor:  0.002
Pgp-substrate:  0.024
Human Intestinal Absorption (HIA):  0.094
20% Bioavailability (F20%):  0.16
30% Bioavailability (F30%):  0.832

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.312
Plasma Protein Binding (PPB):  10.365612030029297%
Volume Distribution (VD):  0.527
Pgp-substrate:  82.9609603881836%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.043
CYP2C19-inhibitor:  0.011
CYP2C19-substrate:  0.087
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.084
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.13
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.031

ADMET: Excretion

Clearance (CL):  2.286
Half-life (T1/2):  0.762

ADMET: Toxicity

hERG Blockers:  0.065
Human Hepatotoxicity (H-HT):  0.053
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.06
Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.003
Skin Sensitization:  0.12
Carcinogencity:  0.025
Eye Corrosion:  0.022
Eye Irritation:  0.956
Respiratory Toxicity:  0.014

Download Data

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

  Natural Product: NPC33415

Natural Product ID:  NPC33415
Common Name*:   E968
IUPAC Name:   (2S,3R)-butane-1,2,3,4-tetrol
Synonyms:   E968
Standard InCHIKey:  UNXHWFMMPAWVPI-ZXZARUISSA-N
Standard InCHI:  InChI=1S/C4H10O4/c5-1-3(7)4(8)2-6/h3-8H,1-2H2/t3-,4+
SMILES:  OC[C@H]([C@H](CO)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL349605
PubChem CID:   222285
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002210] Sugar alcohols

*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
NPO21556 NPC33415 n.a. Sclerotia 0.800 ± 0.203 n.a. n.a. % PMID[20527951]

☑ 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
NPT56 Individual Protein Beta-lactamase AmpC Escherichia coli K-12 Potency = 281.8 nM PMID[501098]
NPT2 Others Unspecified Km = 260000.0 nM PMID[501097]
NPT2 Others Unspecified k cat = 230.0 s-1 PMID[501097]
NPT2 Others Unspecified Km = 880000.0 nM PMID[501097]
NPT920 Individual Protein Alpha-synuclein Homo sapiens Potency n.a. 35481.3 nM PMID[501098]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -2.81 % PMID[501099]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Hit score = 0.1573 n.a. PMID[501100]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 33.21 % PMID[501101]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 5.831 % PMID[501102]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 0.02 % PMID[501103]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.19 % PMID[501104]
NPT2 Others Unspecified Potency n.a. 19534.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 2191.8 nM PubChem BioAssay data set

☑ 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 NPC33415 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
1.0 High Similarity NPC301586
0.9615 High Similarity NPC320326
0.8966 High Similarity NPC182541
0.8966 High Similarity NPC149070
0.8966 High Similarity NPC197207
0.8966 High Similarity NPC187058
0.8966 High Similarity NPC127074
0.8462 Intermediate Similarity NPC157340
0.8148 Intermediate Similarity NPC140389
0.8148 Intermediate Similarity NPC88887
0.8125 Intermediate Similarity NPC325034
0.8125 Intermediate Similarity NPC192065
0.8125 Intermediate Similarity NPC86412
0.8125 Intermediate Similarity NPC293908
0.8125 Intermediate Similarity NPC66052
0.7778 Intermediate Similarity NPC114270
0.7692 Intermediate Similarity NPC219266
0.7188 Intermediate Similarity NPC321170
0.7188 Intermediate Similarity NPC31433
0.7188 Intermediate Similarity NPC266566
0.7143 Intermediate Similarity NPC245688
0.7037 Intermediate Similarity NPC299484
0.7027 Intermediate Similarity NPC111882
0.7027 Intermediate Similarity NPC88278
0.7027 Intermediate Similarity NPC227707
0.7027 Intermediate Similarity NPC99573
0.7027 Intermediate Similarity NPC102981
0.7027 Intermediate Similarity NPC266553
0.7 Intermediate Similarity NPC272307
0.6923 Remote Similarity NPC236761
0.6897 Remote Similarity NPC232554
0.6842 Remote Similarity NPC35661
0.6786 Remote Similarity NPC39977
0.6765 Remote Similarity NPC227267
0.6667 Remote Similarity NPC259982
0.6667 Remote Similarity NPC252154
0.6667 Remote Similarity NPC317060
0.6667 Remote Similarity NPC213159
0.6667 Remote Similarity NPC291502
0.6667 Remote Similarity NPC560
0.6667 Remote Similarity NPC228782
0.6667 Remote Similarity NPC294703
0.6667 Remote Similarity NPC86191
0.6667 Remote Similarity NPC320189
0.6667 Remote Similarity NPC317182
0.6667 Remote Similarity NPC128335
0.6667 Remote Similarity NPC298699
0.6667 Remote Similarity NPC313565
0.6667 Remote Similarity NPC134252
0.6552 Remote Similarity NPC87529
0.6552 Remote Similarity NPC94144
0.6552 Remote Similarity NPC199270
0.65 Remote Similarity NPC29721
0.65 Remote Similarity NPC70756
0.65 Remote Similarity NPC320240
0.641 Remote Similarity NPC24751
0.641 Remote Similarity NPC19044
0.641 Remote Similarity NPC100742
0.641 Remote Similarity NPC121018
0.641 Remote Similarity NPC97444
0.641 Remote Similarity NPC192402
0.6389 Remote Similarity NPC313405
0.6389 Remote Similarity NPC5505
0.6341 Remote Similarity NPC207656
0.6341 Remote Similarity NPC270088
0.6341 Remote Similarity NPC107091
0.6333 Remote Similarity NPC304786
0.6333 Remote Similarity NPC190797
0.6333 Remote Similarity NPC213764
0.6296 Remote Similarity NPC163707
0.625 Remote Similarity NPC325345
0.625 Remote Similarity NPC159845
0.625 Remote Similarity NPC238135
0.6207 Remote Similarity NPC52403
0.619 Remote Similarity NPC69445
0.619 Remote Similarity NPC289758
0.619 Remote Similarity NPC21209
0.619 Remote Similarity NPC176017
0.619 Remote Similarity NPC165846
0.619 Remote Similarity NPC92246
0.619 Remote Similarity NPC255377
0.619 Remote Similarity NPC73906
0.619 Remote Similarity NPC199857
0.619 Remote Similarity NPC285364
0.6154 Remote Similarity NPC149567
0.6154 Remote Similarity NPC320331
0.6129 Remote Similarity NPC329496
0.6129 Remote Similarity NPC230452
0.6129 Remote Similarity NPC317724
0.6111 Remote Similarity NPC168052
0.6111 Remote Similarity NPC191084
0.6111 Remote Similarity NPC250870
0.6061 Remote Similarity NPC270334
0.6061 Remote Similarity NPC110884
0.6047 Remote Similarity NPC88638
0.6047 Remote Similarity NPC321087
0.6047 Remote Similarity NPC230789
0.6047 Remote Similarity NPC277475
0.6047 Remote Similarity NPC314613
0.6047 Remote Similarity NPC252918
0.6 Remote Similarity NPC237965
0.6 Remote Similarity NPC318912
0.6 Remote Similarity NPC256186
0.6 Remote Similarity NPC23071
0.5952 Remote Similarity NPC242655
0.5952 Remote Similarity NPC62014
0.5952 Remote Similarity NPC38891
0.5946 Remote Similarity NPC159089
0.5926 Remote Similarity NPC311000
0.5909 Remote Similarity NPC247546
0.5909 Remote Similarity NPC172086
0.5909 Remote Similarity NPC112363
0.5909 Remote Similarity NPC14144
0.5897 Remote Similarity NPC222792
0.5897 Remote Similarity NPC316217
0.5882 Remote Similarity NPC198126
0.5862 Remote Similarity NPC88839
0.5862 Remote Similarity NPC110344
0.5806 Remote Similarity NPC82694
0.5806 Remote Similarity NPC275462
0.5789 Remote Similarity NPC174396
0.5778 Remote Similarity NPC299781
0.5778 Remote Similarity NPC61270
0.5778 Remote Similarity NPC328954
0.5778 Remote Similarity NPC325822
0.5778 Remote Similarity NPC157193
0.5778 Remote Similarity NPC282143
0.5778 Remote Similarity NPC42503
0.5778 Remote Similarity NPC82512
0.5758 Remote Similarity NPC52362
0.5714 Remote Similarity NPC261351
0.5714 Remote Similarity NPC76217
0.5714 Remote Similarity NPC267243
0.5714 Remote Similarity NPC307739
0.5714 Remote Similarity NPC122962
0.5676 Remote Similarity NPC325165
0.5652 Remote Similarity NPC321394
0.5652 Remote Similarity NPC322158
0.5652 Remote Similarity NPC329128
0.5652 Remote Similarity NPC326283
0.5652 Remote Similarity NPC323574

  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 NPC33415 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 NPD8549 Clinical (unspecified phase)
0.8966 High Similarity NPD8814 Phase 3
0.8462 Intermediate Similarity NPD8226 Approved
0.8125 Intermediate Similarity NPD9053 Approved
0.8125 Intermediate Similarity NPD9051 Approved
0.8125 Intermediate Similarity NPD9052 Approved
0.7778 Intermediate Similarity NPD8225 Phase 3
0.7429 Intermediate Similarity NPD8977 Phase 3
0.7429 Intermediate Similarity NPD8976 Approved
0.7222 Intermediate Similarity NPD9055 Approved
0.7222 Intermediate Similarity NPD9056 Approved
0.7188 Intermediate Similarity NPD8237 Approved
0.7027 Intermediate Similarity NPD8995 Clinical (unspecified phase)
0.7027 Intermediate Similarity NPD8996 Phase 3
0.6875 Remote Similarity NPD8234 Approved
0.6875 Remote Similarity NPD8235 Approved
0.6875 Remote Similarity NPD8236 Phase 1
0.6667 Remote Similarity NPD8957 Approved
0.6667 Remote Similarity NPD8958 Phase 2
0.6667 Remote Similarity NPD8788 Approved
0.65 Remote Similarity NPD9006 Approved
0.641 Remote Similarity NPD8603 Approved
0.641 Remote Similarity NPD8604 Approved
0.641 Remote Similarity NPD8598 Approved
0.641 Remote Similarity NPD8600 Approved
0.641 Remote Similarity NPD8599 Approved
0.641 Remote Similarity NPD8601 Approved
0.641 Remote Similarity NPD8602 Approved
0.641 Remote Similarity NPD8605 Approved
0.6341 Remote Similarity NPD9218 Clinical (unspecified phase)
0.6341 Remote Similarity NPD9219 Approved
0.6296 Remote Similarity NPD8224 Approved
0.625 Remote Similarity NPD8988 Clinical (unspecified phase)
0.619 Remote Similarity NPD8994 Approved
0.619 Remote Similarity NPD8998 Phase 2
0.619 Remote Similarity NPD9000 Phase 3
0.619 Remote Similarity NPD8997 Approved
0.619 Remote Similarity NPD8993 Phase 1
0.619 Remote Similarity NPD8999 Phase 3
0.6154 Remote Similarity NPD7374 Approved
0.5926 Remote Similarity NPD8223 Approved
0.5909 Remote Similarity NPD9003 Clinical (unspecified phase)
0.5909 Remote Similarity NPD9139 Approved
0.5909 Remote Similarity NPD9005 Phase 3
0.5909 Remote Similarity NPD9004 Approved
0.5909 Remote Similarity NPD8965 Approved
0.5909 Remote Similarity NPD8966 Approved
0.5882 Remote Similarity NPD8585 Approved
0.5882 Remote Similarity NPD8586 Approved
0.5882 Remote Similarity NPD8618 Approved
0.5806 Remote Similarity NPD8207 Approved
0.5778 Remote Similarity NPD9669 Clinical (unspecified phase)
0.5778 Remote Similarity NPD8964 Approved
0.5778 Remote Similarity NPD9061 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8205 Approved
0.5714 Remote Similarity NPD8202 Approved
0.5652 Remote Similarity NPD9678 Approved
0.5652 Remote Similarity NPD9677 Phase 3
0.5625 Remote Similarity NPD8219 Approved
0.5625 Remote Similarity NPD8220 Approved
0.561 Remote Similarity NPD8967 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