Structure

Physi-Chem Properties

Molecular Weight:  212.12
Volume:  207.495
LogP:  -2.422
LogD:  -1.391
LogS:  -0.979
# Rotatable Bonds:  3
TPSA:  69.64
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.666
Synthetic Accessibility Score:  2.9
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:  -5.885
MDCK Permeability:  1.493787294748472e-05
Pgp-inhibitor:  0.046
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.879
20% Bioavailability (F20%):  0.091
30% Bioavailability (F30%):  0.236

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.36
Plasma Protein Binding (PPB):  11.968814849853516%
Volume Distribution (VD):  0.574
Pgp-substrate:  93.45030975341797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.077
CYP2C19-inhibitor:  0.036
CYP2C19-substrate:  0.082
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.454
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.292
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.023

ADMET: Excretion

Clearance (CL):  4.803
Half-life (T1/2):  0.728

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.881
Drug-inuced Liver Injury (DILI):  0.725
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.036
Maximum Recommended Daily Dose:  0.066
Skin Sensitization:  0.199
Carcinogencity:  0.031
Eye Corrosion:  0.004
Eye Irritation:  0.018
Respiratory Toxicity:  0.098

Download Data

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

  Natural Product: NPC320221

Natural Product ID:  NPC320221
Common Name*:   Pro-Pro
IUPAC Name:   (2S)-1-[(2S)-pyrrolidin-1-ium-2-carbonyl]pyrrolidine-2-carboxylate
Synonyms:   Pro-Pro
Standard InCHIKey:  RWCOTTLHDJWHRS-YUMQZZPRSA-N
Standard InCHI:  InChI=1S/C10H16N2O3/c13-9(7-3-1-5-11-7)12-6-2-4-8(12)10(14)15/h7-8,11H,1-6H2,(H,14,15)/t7-,8-/m0/s1
SMILES:  OC(=O)[C@@H]1CCCN1C(=O)[C@@H]1CCCN1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL371194
PubChem CID:   11902928
11622593
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:0000348] Peptides
            • [CHEMONTID:0004830] Dipeptides

*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
NPO30193 Mycoplasma genitalium Species Mycoplasmataceae Bacteria n.a. n.a. n.a. PMID[22817898]

☑ 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
NPT1237 Individual Protein Oligopeptide transporter small intestine isoform Homo sapiens Ki = 1200000.0 nM PMID[504208]
NPT1237 Individual Protein Oligopeptide transporter small intestine isoform Homo sapiens EC50 = 700000.0 nM PMID[504209]
NPT1237 Individual Protein Oligopeptide transporter small intestine isoform Homo sapiens max activation = 116.0 % PMID[504209]
NPT1237 Individual Protein Oligopeptide transporter small intestine isoform Homo sapiens IC50 = 800000.0 nM PMID[504209]
NPT1237 Individual Protein Oligopeptide transporter small intestine isoform Homo sapiens Ratio = 170.0 n.a. PMID[504209]

☑ 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 NPC320221 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
0.9118 High Similarity NPC322274
0.8955 High Similarity NPC287693
0.875 High Similarity NPC327272
0.791 Intermediate Similarity NPC11433
0.791 Intermediate Similarity NPC245346
0.791 Intermediate Similarity NPC302003
0.7125 Intermediate Similarity NPC59867
0.7067 Intermediate Similarity NPC196359
0.7067 Intermediate Similarity NPC78312
0.7067 Intermediate Similarity NPC135539
0.7067 Intermediate Similarity NPC221764
0.7051 Intermediate Similarity NPC29326
0.6912 Remote Similarity NPC333075
0.6912 Remote Similarity NPC274499
0.6912 Remote Similarity NPC8488
0.6883 Remote Similarity NPC15864
0.6786 Remote Similarity NPC475542
0.6761 Remote Similarity NPC278209
0.675 Remote Similarity NPC161774
0.675 Remote Similarity NPC209156
0.675 Remote Similarity NPC256312
0.675 Remote Similarity NPC266888
0.6711 Remote Similarity NPC128005
0.6711 Remote Similarity NPC84182
0.6709 Remote Similarity NPC196007
0.6709 Remote Similarity NPC76297
0.6709 Remote Similarity NPC214532
0.6667 Remote Similarity NPC133183
0.6622 Remote Similarity NPC118429
0.6579 Remote Similarity NPC160661
0.6575 Remote Similarity NPC64250
0.6575 Remote Similarity NPC276928
0.6575 Remote Similarity NPC268927
0.6567 Remote Similarity NPC140872
0.6567 Remote Similarity NPC93081
0.6533 Remote Similarity NPC243964
0.6489 Remote Similarity NPC117829
0.6486 Remote Similarity NPC177191
0.6447 Remote Similarity NPC103130
0.6447 Remote Similarity NPC226453
0.6353 Remote Similarity NPC312315
0.6322 Remote Similarity NPC53858
0.6322 Remote Similarity NPC84128
0.63 Remote Similarity NPC128303
0.6296 Remote Similarity NPC470781
0.6296 Remote Similarity NPC328457
0.6282 Remote Similarity NPC327985
0.6238 Remote Similarity NPC241394
0.6237 Remote Similarity NPC474576
0.6237 Remote Similarity NPC477538
0.6207 Remote Similarity NPC470783
0.6196 Remote Similarity NPC275715
0.617 Remote Similarity NPC471098
0.617 Remote Similarity NPC173763
0.617 Remote Similarity NPC62263
0.6147 Remote Similarity NPC469899
0.6145 Remote Similarity NPC126186
0.6129 Remote Similarity NPC475801
0.6129 Remote Similarity NPC474593
0.6044 Remote Similarity NPC477539
0.6044 Remote Similarity NPC469363
0.6044 Remote Similarity NPC69374
0.6044 Remote Similarity NPC90476
0.6022 Remote Similarity NPC322966
0.6 Remote Similarity NPC470782
0.6 Remote Similarity NPC324825
0.6 Remote Similarity NPC112890
0.6 Remote Similarity NPC316231
0.6 Remote Similarity NPC189301
0.6 Remote Similarity NPC176164
0.5977 Remote Similarity NPC31756
0.5949 Remote Similarity NPC278881
0.5926 Remote Similarity NPC107224
0.5921 Remote Similarity NPC320598
0.5921 Remote Similarity NPC254541
0.5918 Remote Similarity NPC473597
0.5909 Remote Similarity NPC476156
0.5909 Remote Similarity NPC476117
0.5909 Remote Similarity NPC476243
0.5909 Remote Similarity NPC476137
0.5895 Remote Similarity NPC476019
0.589 Remote Similarity NPC279661
0.589 Remote Similarity NPC183845
0.5882 Remote Similarity NPC118459
0.5882 Remote Similarity NPC327698
0.5875 Remote Similarity NPC325534
0.5843 Remote Similarity NPC476302
0.5833 Remote Similarity NPC155156
0.5833 Remote Similarity NPC200550
0.5823 Remote Similarity NPC57420
0.5821 Remote Similarity NPC276294
0.58 Remote Similarity NPC475440
0.5773 Remote Similarity NPC301010
0.5769 Remote Similarity NPC314510
0.5735 Remote Similarity NPC198301
0.5714 Remote Similarity NPC316826
0.5714 Remote Similarity NPC321468
0.5714 Remote Similarity NPC317143
0.5714 Remote Similarity NPC280066
0.5714 Remote Similarity NPC327748
0.5714 Remote Similarity NPC321536
0.5676 Remote Similarity NPC272396
0.5673 Remote Similarity NPC323720
0.5667 Remote Similarity NPC23984
0.5658 Remote Similarity NPC317147
0.5658 Remote Similarity NPC318260
0.5657 Remote Similarity NPC40663
0.5652 Remote Similarity NPC472351
0.5647 Remote Similarity NPC185084
0.5644 Remote Similarity NPC220234
0.5641 Remote Similarity NPC329564
0.5641 Remote Similarity NPC327170
0.5641 Remote Similarity NPC143722
0.5631 Remote Similarity NPC475149
0.5631 Remote Similarity NPC471097
0.5625 Remote Similarity NPC315744
0.56 Remote Similarity NPC3604

  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 NPC320221 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
0.8451 Intermediate Similarity NPD2220 Clinical (unspecified phase)
0.791 Intermediate Similarity NPD8865 Approved
0.7412 Intermediate Similarity NPD3177 Phase 3
0.7356 Intermediate Similarity NPD2682 Approved
0.7317 Intermediate Similarity NPD1125 Discovery
0.7237 Intermediate Similarity NPD9649 Approved
0.7195 Intermediate Similarity NPD7762 Phase 2
0.7195 Intermediate Similarity NPD7763 Phase 2
0.7159 Intermediate Similarity NPD4261 Phase 1
0.7067 Intermediate Similarity NPD8868 Approved
0.7042 Intermediate Similarity NPD378 Phase 3
0.6977 Remote Similarity NPD7759 Phase 2
0.6977 Remote Similarity NPD7760 Phase 2
0.6882 Remote Similarity NPD3715 Approved
0.6882 Remote Similarity NPD3713 Approved
0.6882 Remote Similarity NPD8038 Phase 2
0.6882 Remote Similarity NPD3714 Approved
0.6744 Remote Similarity NPD9577 Approved
0.6667 Remote Similarity NPD7841 Clinical (unspecified phase)
0.6622 Remote Similarity NPD9014 Approved
0.6567 Remote Similarity NPD8809 Approved
0.6567 Remote Similarity NPD8808 Approved
0.6548 Remote Similarity NPD617 Approved
0.6512 Remote Similarity NPD2683 Discontinued
0.6447 Remote Similarity NPD9048 Approved
0.6447 Remote Similarity NPD9045 Approved
0.6447 Remote Similarity NPD9046 Phase 3
0.6447 Remote Similarity NPD9047 Approved
0.641 Remote Similarity NPD9232 Phase 2
0.641 Remote Similarity NPD9233 Phase 3
0.641 Remote Similarity NPD9231 Phase 3
0.6351 Remote Similarity NPD9671 Phase 2
0.6351 Remote Similarity NPD9670 Phase 2
0.6329 Remote Similarity NPD322 Phase 1
0.6301 Remote Similarity NPD9425 Approved
0.625 Remote Similarity NPD620 Approved
0.6164 Remote Similarity NPD1456 Approved
0.6145 Remote Similarity NPD366 Approved
0.6125 Remote Similarity NPD9451 Clinical (unspecified phase)
0.6067 Remote Similarity NPD614 Discontinued
0.6 Remote Similarity NPD9044 Approved
0.6 Remote Similarity NPD9666 Clinical (unspecified phase)
0.6 Remote Similarity NPD9665 Clinical (unspecified phase)
0.5976 Remote Similarity NPD1439 Clinical (unspecified phase)
0.5934 Remote Similarity NPD9401 Discovery
0.5918 Remote Similarity NPD1784 Approved
0.59 Remote Similarity NPD6120 Clinical (unspecified phase)
0.5875 Remote Similarity NPD8952 Approved
0.5806 Remote Similarity NPD3176 Clinical (unspecified phase)
0.58 Remote Similarity NPD4825 Clinical (unspecified phase)
0.5789 Remote Similarity NPD8784 Clinical (unspecified phase)
0.5775 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5775 Remote Similarity NPD8950 Approved
0.5733 Remote Similarity NPD8981 Clinical (unspecified phase)
0.5733 Remote Similarity NPD4281 Clinical (unspecified phase)
0.5733 Remote Similarity NPD8979 Approved
0.5733 Remote Similarity NPD8980 Approved
0.5699 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5625 Remote Similarity NPD1782 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