Structure

Physi-Chem Properties

Molecular Weight:  200.08
Volume:  181.693
LogP:  -1.51
LogD:  -1.962
LogS:  -0.914
# Rotatable Bonds:  1
TPSA:  89.87
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.434
Synthetic Accessibility Score:  3.544
Fsp3:  0.75
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:  -5.859
MDCK Permeability:  0.001017088070511818
Pgp-inhibitor:  0.0
Pgp-substrate:  0.342
Human Intestinal Absorption (HIA):  0.168
20% Bioavailability (F20%):  0.923
30% Bioavailability (F30%):  0.581

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.094
Plasma Protein Binding (PPB):  7.674354076385498%
Volume Distribution (VD):  0.536
Pgp-substrate:  93.18986511230469%

ADMET: Metabolism

CYP1A2-inhibitor:  0.006
CYP1A2-substrate:  0.058
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.12
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.336
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.147
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.046

ADMET: Excretion

Clearance (CL):  2.079
Half-life (T1/2):  0.608

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.829
Drug-inuced Liver Injury (DILI):  0.638
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.036
Maximum Recommended Daily Dose:  0.744
Skin Sensitization:  0.212
Carcinogencity:  0.035
Eye Corrosion:  0.003
Eye Irritation:  0.03
Respiratory Toxicity:  0.063

Download Data

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

  Natural Product: NPC470782

Natural Product ID:  NPC470782
Common Name*:   (3S,7R,8As)-7-Hydroxy-3-(Hydroxymethyl)Hexahydropyrrolo[1,2-A]Pyrazine-1,4-Dione
IUPAC Name:   (3S,7R,8aS)-7-hydroxy-3-(hydroxymethyl)-2,3,6,7,8,8a-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
Synonyms:  
Standard InCHIKey:  FUYZNZHRVJWTLT-SRQIZXRXSA-N
Standard InCHI:  InChI=1S/C8H12N2O4/c11-3-5-8(14)10-2-4(12)1-6(10)7(13)9-5/h4-6,11-12H,1-3H2,(H,9,13)/t4-,5+,6+/m1/s1
SMILES:  OC[C@@H]1N=C(O)[C@H]2N(C1=O)C[C@@H](C2)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2229108
PubChem CID:   9815587
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

*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
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17616609]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17929896]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19113967]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19159274]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19256529]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. isolated from sediment collected using a hand held deep water sampling device at >33 m depth in Vanuatu 2003 PMID[20303767]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21667925]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21954885]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22106303]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota stem bark of Melia azedarach n.a. n.a. PMID[22409377]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23557488]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23563483]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[7622436]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota 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
NPT1240 Individual Protein Solute carrier family 15 member 1 Rattus norvegicus Ratio = 2.5 n.a. PMID[537269]
NPT1237 Individual Protein Oligopeptide transporter small intestine isoform Homo sapiens Km = 2530000.0 nM PMID[537269]
NPT1237 Individual Protein Oligopeptide transporter small intestine isoform Homo sapiens IC50 = 18200000.0 nM PMID[537269]
NPT1237 Individual Protein Oligopeptide transporter small intestine isoform Homo sapiens Ki = 36000000.0 nM PMID[537269]
NPT176 Organism Artemia salina Artemia salina LC50 > 100.0 ug.mL-1 PMID[537268]
NPT35 Others n.a. T1/2 > 20.0 hr PMID[537269]
NPT27 Others Unspecified T1/2 > 20.0 hr PMID[537269]
NPT27 Others Unspecified F = 85.0 % PMID[537269]
NPT27 Others Unspecified AUCt = 194.0 nM/ml.hr PMID[537269]
NPT27 Others Unspecified Cmax = 334910.0 nM PMID[537269]
NPT27 Others Unspecified T1/2 = 1.13 hr PMID[537269]
NPT27 Others Unspecified AUCt = 81.4 nM/ml.hr PMID[537269]
NPT27 Others Unspecified Cmax = 27840.0 nM PMID[537269]
NPT27 Others Unspecified Tmax = 1.25 hr PMID[537269]
NPT27 Others Unspecified T1/2 = 2.12 hr PMID[537269]
NPT27 Others Unspecified F = 21.0 % PMID[537269]
NPT27 Others Unspecified AUCt = 89.15 nM/ml.hr PMID[537269]
NPT27 Others Unspecified Cmax = 26650.0 nM PMID[537269]
NPT27 Others Unspecified Tmax = 1.5 hr PMID[537269]
NPT27 Others Unspecified T1/2 = 5.23 hr PMID[537269]
NPT27 Others Unspecified T1/2 = 1.5 hr PMID[537269]
NPT27 Others Unspecified Cmax = 95960.0 nM PMID[537269]
NPT27 Others Unspecified AUCt = 323.55 nM/ml.hr PMID[537269]

☑ 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 NPC470782 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
0.9429 High Similarity NPC126186
0.942 High Similarity NPC470781
0.8571 High Similarity NPC470783
0.8429 Intermediate Similarity NPC128005
0.8429 Intermediate Similarity NPC84182
0.8261 Intermediate Similarity NPC243964
0.7875 Intermediate Similarity NPC475542
0.7867 Intermediate Similarity NPC76297
0.7867 Intermediate Similarity NPC214532
0.7867 Intermediate Similarity NPC196007
0.7848 Intermediate Similarity NPC312315
0.7662 Intermediate Similarity NPC161774
0.7662 Intermediate Similarity NPC209156
0.7662 Intermediate Similarity NPC266888
0.7662 Intermediate Similarity NPC256312
0.7407 Intermediate Similarity NPC31756
0.7356 Intermediate Similarity NPC275715
0.7317 Intermediate Similarity NPC476156
0.7317 Intermediate Similarity NPC476117
0.7317 Intermediate Similarity NPC476137
0.7317 Intermediate Similarity NPC476243
0.7229 Intermediate Similarity NPC476302
0.716 Intermediate Similarity NPC329077
0.6951 Remote Similarity NPC59867
0.6889 Remote Similarity NPC475801
0.6889 Remote Similarity NPC474593
0.6875 Remote Similarity NPC29326
0.6818 Remote Similarity NPC477539
0.6813 Remote Similarity NPC474576
0.6739 Remote Similarity NPC62263
0.6739 Remote Similarity NPC173763
0.6739 Remote Similarity NPC471098
0.6735 Remote Similarity NPC476877
0.6632 Remote Similarity NPC473597
0.6632 Remote Similarity NPC134504
0.6632 Remote Similarity NPC47076
0.66 Remote Similarity NPC476876
0.6528 Remote Similarity NPC275727
0.6495 Remote Similarity NPC475440
0.6471 Remote Similarity NPC325902
0.641 Remote Similarity NPC160661
0.6337 Remote Similarity NPC128303
0.6329 Remote Similarity NPC287693
0.6327 Remote Similarity NPC475758
0.6296 Remote Similarity NPC322274
0.6286 Remote Similarity NPC476875
0.6277 Remote Similarity NPC477538
0.6275 Remote Similarity NPC241394
0.6263 Remote Similarity NPC475791
0.6263 Remote Similarity NPC13175
0.6139 Remote Similarity NPC471097
0.6139 Remote Similarity NPC475149
0.6117 Remote Similarity NPC475637
0.6087 Remote Similarity NPC89051
0.6087 Remote Similarity NPC43246
0.6055 Remote Similarity NPC296043
0.6022 Remote Similarity NPC210456
0.6022 Remote Similarity NPC163352
0.6 Remote Similarity NPC315806
0.6 Remote Similarity NPC319753
0.6 Remote Similarity NPC329216
0.6 Remote Similarity NPC320221
0.6 Remote Similarity NPC233034
0.5978 Remote Similarity NPC325723
0.5976 Remote Similarity NPC34291
0.5976 Remote Similarity NPC126664
0.593 Remote Similarity NPC327272
0.5926 Remote Similarity NPC12514
0.5926 Remote Similarity NPC294883
0.5895 Remote Similarity NPC315063
0.5895 Remote Similarity NPC322966
0.5876 Remote Similarity NPC315237
0.5872 Remote Similarity NPC471202
0.5872 Remote Similarity NPC63191
0.5865 Remote Similarity NPC323720
0.5854 Remote Similarity NPC135539
0.5854 Remote Similarity NPC141156
0.5854 Remote Similarity NPC184150
0.5854 Remote Similarity NPC196359
0.5854 Remote Similarity NPC78312
0.5854 Remote Similarity NPC221764
0.5849 Remote Similarity NPC67009
0.5842 Remote Similarity NPC220234
0.5824 Remote Similarity NPC184473
0.5789 Remote Similarity NPC160688
0.5783 Remote Similarity NPC254617
0.5783 Remote Similarity NPC306763
0.5783 Remote Similarity NPC474469
0.5783 Remote Similarity NPC266242
0.5783 Remote Similarity NPC74555
0.5761 Remote Similarity NPC106780
0.5745 Remote Similarity NPC469363
0.5733 Remote Similarity NPC272396
0.5714 Remote Similarity NPC311668
0.5714 Remote Similarity NPC475715
0.5714 Remote Similarity NPC473419
0.5714 Remote Similarity NPC10262
0.5714 Remote Similarity NPC65832
0.5714 Remote Similarity NPC475127
0.5702 Remote Similarity NPC470652
0.5701 Remote Similarity NPC296143
0.5699 Remote Similarity NPC112842
0.5699 Remote Similarity NPC71339
0.569 Remote Similarity NPC50520
0.5679 Remote Similarity NPC57420
0.5679 Remote Similarity NPC145658
0.5673 Remote Similarity NPC5864
0.5673 Remote Similarity NPC301148
0.5673 Remote Similarity NPC124554
0.5663 Remote Similarity NPC59221
0.5657 Remote Similarity NPC36985
0.5657 Remote Similarity NPC17892
0.5652 Remote Similarity NPC315188
0.5652 Remote Similarity NPC84128
0.5652 Remote Similarity NPC53858
0.5647 Remote Similarity NPC163538
0.5647 Remote Similarity NPC115800
0.5625 Remote Similarity NPC8087
0.5625 Remote Similarity NPC62507
0.5619 Remote Similarity NPC198344
0.5614 Remote Similarity NPC469899
0.561 Remote Similarity NPC472609
0.56 Remote Similarity NPC73765
0.56 Remote Similarity NPC283698

  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 NPC470782 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
0.7647 Intermediate Similarity NPD3177 Phase 3
0.7143 Intermediate Similarity NPD2683 Discontinued
0.7011 Intermediate Similarity NPD3723 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD4780 Clinical (unspecified phase)
0.6849 Remote Similarity NPD8951 Approved
0.6813 Remote Similarity NPD4261 Phase 1
0.6795 Remote Similarity NPD322 Phase 1
0.6628 Remote Similarity NPD7763 Phase 2
0.6628 Remote Similarity NPD7762 Phase 2
0.6526 Remote Similarity NPD7841 Clinical (unspecified phase)
0.6438 Remote Similarity NPD1456 Approved
0.6404 Remote Similarity NPD9577 Approved
0.6392 Remote Similarity NPD8038 Phase 2
0.6364 Remote Similarity NPD1125 Discovery
0.6351 Remote Similarity NPD9425 Approved
0.6333 Remote Similarity NPD9401 Discovery
0.6264 Remote Similarity NPD7760 Phase 2
0.6264 Remote Similarity NPD7759 Phase 2
0.6087 Remote Similarity NPD9580 Clinical (unspecified phase)
0.6087 Remote Similarity NPD9581 Clinical (unspecified phase)
0.6078 Remote Similarity NPD6122 Discontinued
0.6024 Remote Similarity NPD2220 Clinical (unspecified phase)
0.6 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6 Remote Similarity NPD9440 Discontinued
0.5977 Remote Similarity NPD9199 Approved
0.5976 Remote Similarity NPD9443 Clinical (unspecified phase)
0.5921 Remote Similarity NPD581 Approved
0.5921 Remote Similarity NPD583 Approved
0.5921 Remote Similarity NPD843 Clinical (unspecified phase)
0.5921 Remote Similarity NPD584 Approved
0.5904 Remote Similarity NPD620 Approved
0.5895 Remote Similarity NPD755 Phase 3
0.5854 Remote Similarity NPD8868 Approved
0.5833 Remote Similarity NPD9565 Discontinued
0.5783 Remote Similarity NPD9444 Discontinued
0.5773 Remote Similarity NPD251 Approved
0.5765 Remote Similarity NPD9446 Approved
0.5747 Remote Similarity NPD9198 Approved
0.5714 Remote Similarity NPD9558 Phase 3
0.5714 Remote Similarity NPD9556 Approved
0.5714 Remote Similarity NPD279 Clinical (unspecified phase)
0.5699 Remote Similarity NPD280 Approved
0.5682 Remote Similarity NPD9407 Approved
0.566 Remote Similarity NPD1385 Discontinued
0.5652 Remote Similarity NPD9560 Approved
0.5652 Remote Similarity NPD9561 Approved
0.5647 Remote Similarity NPD9649 Approved
0.5647 Remote Similarity NPD1439 Clinical (unspecified phase)
0.5638 Remote Similarity NPD9557 Clinical (unspecified phase)
0.5625 Remote Similarity NPD3192 Approved
0.5625 Remote Similarity NPD867 Phase 3
0.5625 Remote Similarity NPD868 Phase 3
0.5625 Remote Similarity NPD3193 Approved
0.5616 Remote Similarity NPD8950 Approved
0.56 Remote Similarity NPD9639 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