Structure

Physi-Chem Properties

Molecular Weight:  210.1
Volume:  198.938
LogP:  -0.796
LogD:  -1.383
LogS:  -1.139
# Rotatable Bonds:  0
TPSA:  60.85
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.555
Synthetic Accessibility Score:  3.405
Fsp3:  0.8
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:  -5.194
MDCK Permeability:  0.00017508711607661098
Pgp-inhibitor:  0.001
Pgp-substrate:  0.085
Human Intestinal Absorption (HIA):  0.227
20% Bioavailability (F20%):  0.495
30% Bioavailability (F30%):  0.308

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.123
Plasma Protein Binding (PPB):  10.15757942199707%
Volume Distribution (VD):  0.765
Pgp-substrate:  84.12580871582031%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.097
CYP2C19-inhibitor:  0.032
CYP2C19-substrate:  0.703
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.573
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.233
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.157

ADMET: Excretion

Clearance (CL):  4.787
Half-life (T1/2):  0.635

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.976
Drug-inuced Liver Injury (DILI):  0.805
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.195
Maximum Recommended Daily Dose:  0.884
Skin Sensitization:  0.3
Carcinogencity:  0.053
Eye Corrosion:  0.003
Eye Irritation:  0.018
Respiratory Toxicity:  0.109

Download Data

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

  Natural Product: NPC29326

Natural Product ID:  NPC29326
Common Name*:   Cyclo-(L-Prolyl-Trans-4-Hydroxy-L-Prolyl)
IUPAC Name:   (2R,5aS,10aS)-2-hydroxy-1,2,3,5a,6,7,8,10a-octahydrodipyrrolo[1,2-c:1',2'-f]pyrazine-5,10-dione
Synonyms:  
Standard InCHIKey:  NUWIAVSANIAUAA-CSMHCCOUSA-N
Standard InCHI:  InChI=1S/C10H14N2O3/c13-6-4-8-10(15)11-3-1-2-7(11)9(14)12(8)5-6/h6-8,13H,1-5H2/t6-,7+,8+/m1/s1
SMILES:  O[C@@H]1C[C@@H]2N(C1)C(=O)[C@H]1N(C2=O)CCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL452412
PubChem CID:   15590503
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
NPO20897.1 Suberites domuncula Under-species n.a. n.a. n.a. n.a. n.a. PMID[15270577]
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
NPT176 Organism Artemia salina Artemia salina LC50 > 100.0 ug.mL-1 PMID[545307]

☑ 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 NPC29326 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
0.7051 Intermediate Similarity NPC126186
0.7051 Intermediate Similarity NPC320221
0.6892 Remote Similarity NPC160661
0.6875 Remote Similarity NPC470782
0.6867 Remote Similarity NPC470783
0.68 Remote Similarity NPC287693
0.6795 Remote Similarity NPC470781
0.6753 Remote Similarity NPC322274
0.6667 Remote Similarity NPC472609
0.6627 Remote Similarity NPC312315
0.6494 Remote Similarity NPC78312
0.6494 Remote Similarity NPC135539
0.6494 Remote Similarity NPC196359
0.6494 Remote Similarity NPC221764
0.6471 Remote Similarity NPC475542
0.6364 Remote Similarity NPC84182
0.6364 Remote Similarity NPC128303
0.6364 Remote Similarity NPC128005
0.6341 Remote Similarity NPC327272
0.63 Remote Similarity NPC241394
0.622 Remote Similarity NPC209156
0.622 Remote Similarity NPC256312
0.622 Remote Similarity NPC161774
0.622 Remote Similarity NPC266888
0.6203 Remote Similarity NPC107224
0.6184 Remote Similarity NPC243964
0.6173 Remote Similarity NPC214532
0.6173 Remote Similarity NPC196007
0.6173 Remote Similarity NPC76297
0.6111 Remote Similarity NPC469363
0.6075 Remote Similarity NPC271115
0.6038 Remote Similarity NPC309731
0.6026 Remote Similarity NPC233034
0.6 Remote Similarity NPC59867
0.5972 Remote Similarity NPC277072
0.5972 Remote Similarity NPC178263
0.5957 Remote Similarity NPC474576
0.5934 Remote Similarity NPC477539
0.5914 Remote Similarity NPC275715
0.5895 Remote Similarity NPC62263
0.5895 Remote Similarity NPC173763
0.5895 Remote Similarity NPC471098
0.5872 Remote Similarity NPC28542
0.5862 Remote Similarity NPC31756
0.5859 Remote Similarity NPC475440
0.5851 Remote Similarity NPC474593
0.5851 Remote Similarity NPC475801
0.5816 Remote Similarity NPC473597
0.5806 Remote Similarity NPC168017
0.5802 Remote Similarity NPC126664
0.5802 Remote Similarity NPC171850
0.5802 Remote Similarity NPC474469
0.5802 Remote Similarity NPC34291
0.5795 Remote Similarity NPC476117
0.5795 Remote Similarity NPC476156
0.5795 Remote Similarity NPC476243
0.5795 Remote Similarity NPC476137
0.575 Remote Similarity NPC294883
0.575 Remote Similarity NPC12514
0.5747 Remote Similarity NPC233108
0.5745 Remote Similarity NPC322966
0.5732 Remote Similarity NPC475715
0.5732 Remote Similarity NPC473419
0.5732 Remote Similarity NPC475127
0.573 Remote Similarity NPC476302
0.5714 Remote Similarity NPC185084
0.5684 Remote Similarity NPC178632
0.5679 Remote Similarity NPC184150
0.5679 Remote Similarity NPC141156
0.5679 Remote Similarity NPC59221
0.5676 Remote Similarity NPC471423
0.5676 Remote Similarity NPC275727
0.5676 Remote Similarity NPC471442
0.5673 Remote Similarity NPC475637
0.5664 Remote Similarity NPC266910
0.5658 Remote Similarity NPC302003
0.5658 Remote Similarity NPC11433
0.5658 Remote Similarity NPC245346
0.5616 Remote Similarity NPC333075
0.5616 Remote Similarity NPC274499
0.5616 Remote Similarity NPC8488
0.561 Remote Similarity NPC266242
0.561 Remote Similarity NPC306763
0.561 Remote Similarity NPC74555
0.561 Remote Similarity NPC254617

  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 NPC29326 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
0.7093 Intermediate Similarity NPD3177 Phase 3
0.6883 Remote Similarity NPD2220 Clinical (unspecified phase)
0.6744 Remote Similarity NPD9401 Discovery
0.6494 Remote Similarity NPD8868 Approved
0.6471 Remote Similarity NPD7762 Phase 2
0.6471 Remote Similarity NPD7763 Phase 2
0.641 Remote Similarity NPD322 Phase 1
0.6216 Remote Similarity NPD8951 Approved
0.6211 Remote Similarity NPD7841 Clinical (unspecified phase)
0.6129 Remote Similarity NPD4261 Phase 1
0.6049 Remote Similarity NPD9649 Approved
0.6027 Remote Similarity NPD1456 Approved
0.6026 Remote Similarity NPD9440 Discontinued
0.5946 Remote Similarity NPD9425 Approved
0.5918 Remote Similarity NPD8038 Phase 2
0.5889 Remote Similarity NPD9577 Approved
0.5854 Remote Similarity NPD1439 Clinical (unspecified phase)
0.5802 Remote Similarity NPD9443 Clinical (unspecified phase)
0.5789 Remote Similarity NPD378 Phase 3
0.5732 Remote Similarity NPD620 Approved
0.5714 Remote Similarity NPD9455 Approved
0.5667 Remote Similarity NPD2683 Discontinued
0.5667 Remote Similarity NPD1125 Discovery
0.5658 Remote Similarity NPD605 Clinical (unspecified phase)
0.5658 Remote Similarity NPD8865 Approved
0.5641 Remote Similarity NPD3192 Approved
0.5641 Remote Similarity NPD3193 Approved
0.5641 Remote Similarity NPD393 Approved
0.5631 Remote Similarity NPD6122 Discontinued
0.5625 Remote Similarity NPD4780 Clinical (unspecified phase)
0.561 Remote Similarity NPD9444 Discontinued
0.5604 Remote Similarity NPD883 Phase 2
0.5604 Remote Similarity NPD882 Phase 2
0.5604 Remote Similarity NPD614 Discontinued

  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