Structure

Physi-Chem Properties

Molecular Weight:  204.07
Volume:  187.664
LogP:  -3.954
LogD:  -1.383
LogS:  -1.181
# Rotatable Bonds:  7
TPSA:  129.72
# H-Bond Aceptor:  7
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.411
Synthetic Accessibility Score:  2.449
Fsp3:  0.571
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:  -6.219
MDCK Permeability:  0.0036014632787555456
Pgp-inhibitor:  0.0
Pgp-substrate:  0.033
Human Intestinal Absorption (HIA):  0.04
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.326
Plasma Protein Binding (PPB):  11.90597152709961%
Volume Distribution (VD):  0.325
Pgp-substrate:  85.38194274902344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.014
CYP2C19-inhibitor:  0.044
CYP2C19-substrate:  0.037
CYP2C9-inhibitor:  0.11
CYP2C9-substrate:  0.49
CYP2D6-inhibitor:  0.017
CYP2D6-substrate:  0.145
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.004

ADMET: Excretion

Clearance (CL):  3.596
Half-life (T1/2):  0.638

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.025
Drug-inuced Liver Injury (DILI):  0.008
AMES Toxicity:  0.026
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.005
Skin Sensitization:  0.166
Carcinogencity:  0.015
Eye Corrosion:  0.003
Eye Irritation:  0.074
Respiratory Toxicity:  0.042

Download Data

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

  Natural Product: NPC325985

Natural Product ID:  NPC325985
Common Name*:   (2R)-2-Amino-5-(Carboxymethylamino)-5-Oxopentanoic Acid
IUPAC Name:   (2R)-2-amino-5-(carboxymethylamino)-5-oxopentanoic acid
Synonyms:  
Standard InCHIKey:  ACIJGUBIMXQCMF-SCSAIBSYSA-N
Standard InCHI:  InChI=1S/C7H12N2O5/c8-4(7(13)14)1-2-5(10)9-3-6(11)12/h4H,1-3,8H2,(H,9,10)(H,11,12)(H,13,14)/t4-/m1/s1
SMILES:  C(CC(=O)NCC(=O)O)C(C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1512275
PubChem CID:   6604701
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
NPO30940 Bas taurus n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]

☑ 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
NPT53 Individual Protein "4'-phosphopantetheinyl transferase ffp" Bacillus subtilis Potency = 100000.0 nM PMID[543617]
NPT199 Individual Protein DNA polymerase kappa Homo sapiens Potency n.a. 21192.3 nM PMID[543618]
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency n.a. 1678.9 nM PMID[543617]
NPT49 Individual Protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 22387.2 nM PMID[543618]
NPT533 Protein-Protein Interaction Runt-related transcription factor 1/Core-binding factor subunit beta Homo sapiens Potency n.a. 3981.1 nM PMID[543618]

☑ 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 NPC325985 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
0.9615 High Similarity NPC38463
0.9444 High Similarity NPC321536
0.9423 High Similarity NPC322573
0.9412 High Similarity NPC197087
0.9412 High Similarity NPC190184
0.9273 High Similarity NPC143722
0.8793 High Similarity NPC289691
0.8644 High Similarity NPC174304
0.8644 High Similarity NPC325597
0.8333 Intermediate Similarity NPC263065
0.8333 Intermediate Similarity NPC189178
0.8302 Intermediate Similarity NPC273330
0.8302 Intermediate Similarity NPC137958
0.8226 Intermediate Similarity NPC319046
0.8148 Intermediate Similarity NPC29950
0.8148 Intermediate Similarity NPC19576
0.8103 Intermediate Similarity NPC327748
0.8103 Intermediate Similarity NPC320598
0.8103 Intermediate Similarity NPC316826
0.8103 Intermediate Similarity NPC317143
0.8103 Intermediate Similarity NPC321468
0.8103 Intermediate Similarity NPC254541
0.8095 Intermediate Similarity NPC126779
0.7966 Intermediate Similarity NPC329564
0.7966 Intermediate Similarity NPC327170
0.7963 Intermediate Similarity NPC327239
0.7931 Intermediate Similarity NPC189301
0.7931 Intermediate Similarity NPC176164
0.7885 Intermediate Similarity NPC297220
0.7778 Intermediate Similarity NPC118524
0.7759 Intermediate Similarity NPC317147
0.7759 Intermediate Similarity NPC318260
0.7719 Intermediate Similarity NPC2801
0.7719 Intermediate Similarity NPC327831
0.7705 Intermediate Similarity NPC327252
0.7692 Intermediate Similarity NPC118459
0.7692 Intermediate Similarity NPC327698
0.7593 Intermediate Similarity NPC140872
0.7593 Intermediate Similarity NPC153370
0.7593 Intermediate Similarity NPC93081
0.7544 Intermediate Similarity NPC316889
0.7544 Intermediate Similarity NPC321118
0.7455 Intermediate Similarity NPC112890
0.7455 Intermediate Similarity NPC324825
0.7455 Intermediate Similarity NPC316231
0.7455 Intermediate Similarity NPC328378
0.7368 Intermediate Similarity NPC329495
0.7358 Intermediate Similarity NPC329263
0.7344 Intermediate Similarity NPC325534
0.7193 Intermediate Similarity NPC322946
0.7143 Intermediate Similarity NPC84636
0.7143 Intermediate Similarity NPC162620
0.7143 Intermediate Similarity NPC62045
0.7143 Intermediate Similarity NPC245027
0.7143 Intermediate Similarity NPC226027
0.7143 Intermediate Similarity NPC174246
0.7143 Intermediate Similarity NPC43204
0.7097 Intermediate Similarity NPC68974
0.7018 Intermediate Similarity NPC319175
0.6957 Remote Similarity NPC315897
0.6949 Remote Similarity NPC279661
0.6949 Remote Similarity NPC183845
0.6923 Remote Similarity NPC326992
0.6923 Remote Similarity NPC168375
0.6923 Remote Similarity NPC121517
0.6885 Remote Similarity NPC278209
0.6825 Remote Similarity NPC321419
0.6812 Remote Similarity NPC328457
0.6769 Remote Similarity NPC88898
0.6769 Remote Similarity NPC106216
0.6719 Remote Similarity NPC118429
0.6667 Remote Similarity NPC227850
0.6667 Remote Similarity NPC291186
0.6667 Remote Similarity NPC167986
0.6667 Remote Similarity NPC276294
0.6667 Remote Similarity NPC50047
0.6667 Remote Similarity NPC69179
0.6567 Remote Similarity NPC470108
0.6545 Remote Similarity NPC132307
0.6545 Remote Similarity NPC325097
0.6545 Remote Similarity NPC126925
0.6545 Remote Similarity NPC323974
0.6538 Remote Similarity NPC18188
0.6522 Remote Similarity NPC472579
0.6515 Remote Similarity NPC315744
0.6515 Remote Similarity NPC103130
0.6515 Remote Similarity NPC226453
0.6508 Remote Similarity NPC302003
0.6508 Remote Similarity NPC245346
0.6508 Remote Similarity NPC11433
0.6491 Remote Similarity NPC136159
0.6471 Remote Similarity NPC222327
0.6471 Remote Similarity NPC470109
0.6471 Remote Similarity NPC188231
0.6441 Remote Similarity NPC125736
0.6429 Remote Similarity NPC208793
0.6429 Remote Similarity NPC285322
0.6418 Remote Similarity NPC278881
0.6406 Remote Similarity NPC268927
0.6406 Remote Similarity NPC276928
0.6406 Remote Similarity NPC64250
0.6389 Remote Similarity NPC476248
0.6377 Remote Similarity NPC81647
0.6377 Remote Similarity NPC470110
0.6351 Remote Similarity NPC59867
0.6333 Remote Similarity NPC200550
0.6333 Remote Similarity NPC155156
0.6324 Remote Similarity NPC327985
0.6316 Remote Similarity NPC213876
0.6316 Remote Similarity NPC49952
0.6316 Remote Similarity NPC185755
0.6316 Remote Similarity NPC136476
0.6308 Remote Similarity NPC177191
0.6296 Remote Similarity NPC66043
0.6296 Remote Similarity NPC53449
0.6296 Remote Similarity NPC326212
0.6296 Remote Similarity NPC237525
0.6267 Remote Similarity NPC314680
0.625 Remote Similarity NPC198301
0.625 Remote Similarity NPC190385
0.625 Remote Similarity NPC55274
0.6207 Remote Similarity NPC101249
0.6167 Remote Similarity NPC315977
0.6154 Remote Similarity NPC116709
0.6154 Remote Similarity NPC53858
0.6154 Remote Similarity NPC272614
0.6154 Remote Similarity NPC21290
0.6154 Remote Similarity NPC84128
0.6129 Remote Similarity NPC322091
0.6129 Remote Similarity NPC60672
0.6111 Remote Similarity NPC327250
0.6066 Remote Similarity NPC202525
0.6056 Remote Similarity NPC133183
0.6053 Remote Similarity NPC37681
0.6038 Remote Similarity NPC63621
0.6034 Remote Similarity NPC248970
0.6034 Remote Similarity NPC306238
0.6034 Remote Similarity NPC309658
0.6029 Remote Similarity NPC145658
0.6029 Remote Similarity NPC57420
0.6026 Remote Similarity NPC475542
0.6026 Remote Similarity NPC314466
0.6 Remote Similarity NPC152451
0.6 Remote Similarity NPC93888
0.6 Remote Similarity NPC193989
0.6 Remote Similarity NPC270805
0.6 Remote Similarity NPC170739
0.5972 Remote Similarity NPC478256
0.597 Remote Similarity NPC322206
0.597 Remote Similarity NPC477644
0.5968 Remote Similarity NPC245768
0.5938 Remote Similarity NPC313263
0.5932 Remote Similarity NPC181588
0.5909 Remote Similarity NPC473599
0.5902 Remote Similarity NPC114990
0.5902 Remote Similarity NPC329181
0.5902 Remote Similarity NPC319110
0.5902 Remote Similarity NPC50457
0.5857 Remote Similarity NPC287693
0.5844 Remote Similarity NPC191774
0.5833 Remote Similarity NPC322274
0.5833 Remote Similarity NPC327542
0.5806 Remote Similarity NPC155512
0.5802 Remote Similarity NPC95478
0.5802 Remote Similarity NPC145748
0.5802 Remote Similarity NPC155670
0.5781 Remote Similarity NPC102815
0.5781 Remote Similarity NPC10915
0.5775 Remote Similarity NPC221764
0.5775 Remote Similarity NPC196359
0.5775 Remote Similarity NPC78312
0.5775 Remote Similarity NPC135539
0.5765 Remote Similarity NPC477729
0.5753 Remote Similarity NPC476285
0.5753 Remote Similarity NPC477642
0.5753 Remote Similarity NPC476291
0.5738 Remote Similarity NPC80350
0.5738 Remote Similarity NPC17244
0.5732 Remote Similarity NPC227051
0.5714 Remote Similarity NPC262615
0.5714 Remote Similarity NPC315780
0.5714 Remote Similarity NPC472594
0.5714 Remote Similarity NPC317815
0.5694 Remote Similarity NPC107224
0.569 Remote Similarity NPC43264
0.5667 Remote Similarity NPC316168
0.5667 Remote Similarity NPC204364
0.5641 Remote Similarity NPC316242
0.5625 Remote Similarity NPC219340
0.5616 Remote Similarity NPC473985
0.5616 Remote Similarity NPC28348
0.5616 Remote Similarity NPC474299
0.5616 Remote Similarity NPC475808
0.5616 Remote Similarity NPC474298
0.5616 Remote Similarity NPC15864
0.5614 Remote Similarity NPC110533
0.5614 Remote Similarity NPC317691
0.5614 Remote Similarity NPC326808
0.5614 Remote Similarity NPC254482
0.5614 Remote Similarity NPC226265

  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 NPC325985 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
0.9623 High Similarity NPD9433 Approved
0.9412 High Similarity NPD8785 Approved
0.8644 High Similarity NPD348 Approved
0.8361 Intermediate Similarity NPD886 Clinical (unspecified phase)
0.8361 Intermediate Similarity NPD1429 Clinical (unspecified phase)
0.8333 Intermediate Similarity NPD9205 Approved
0.8333 Intermediate Similarity NPD9204 Approved
0.8302 Intermediate Similarity NPD8872 Phase 3
0.8302 Intermediate Similarity NPD8871 Approved
0.8226 Intermediate Similarity NPD337 Discontinued
0.8226 Intermediate Similarity NPD4241 Registered
0.8148 Intermediate Similarity NPD61 Approved
0.8148 Intermediate Similarity NPD8847 Approved
0.8148 Intermediate Similarity NPD8846 Approved
0.8095 Intermediate Similarity NPD4242 Approved
0.8 Intermediate Similarity NPD8851 Phase 1
0.7846 Intermediate Similarity NPD2262 Clinical (unspecified phase)
0.7833 Intermediate Similarity NPD574 Approved
0.7727 Intermediate Similarity NPD6944 Clinical (unspecified phase)
0.7705 Intermediate Similarity NPD575 Clinical (unspecified phase)
0.7593 Intermediate Similarity NPD8808 Approved
0.7593 Intermediate Similarity NPD8809 Approved
0.7593 Intermediate Similarity NPD8614 Approved
0.7455 Intermediate Similarity NPD9044 Approved
0.7344 Intermediate Similarity NPD8952 Approved
0.7206 Intermediate Similarity NPD1147 Phase 2
0.7193 Intermediate Similarity NPD9441 Phase 2
0.7143 Intermediate Similarity NPD9016 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD9018 Approved
0.7143 Intermediate Similarity NPD9017 Approved
0.6957 Remote Similarity NPD1825 Clinical (unspecified phase)
0.6857 Remote Similarity NPD366 Approved
0.6719 Remote Similarity NPD9014 Approved
0.6711 Remote Similarity NPD7643 Phase 1
0.6667 Remote Similarity NPD8805 Approved
0.6667 Remote Similarity NPD8804 Approved
0.6618 Remote Similarity NPD9451 Clinical (unspecified phase)
0.6545 Remote Similarity NPD8798 Approved
0.6545 Remote Similarity NPD9019 Approved
0.6538 Remote Similarity NPD8623 Phase 1
0.6515 Remote Similarity NPD9045 Approved
0.6515 Remote Similarity NPD9046 Phase 3
0.6515 Remote Similarity NPD9048 Approved
0.6515 Remote Similarity NPD9047 Approved
0.6508 Remote Similarity NPD8865 Approved
0.6471 Remote Similarity NPD8842 Clinical (unspecified phase)
0.6471 Remote Similarity NPD9421 Phase 1
0.6452 Remote Similarity NPD8980 Approved
0.6452 Remote Similarity NPD8979 Approved
0.6452 Remote Similarity NPD8981 Clinical (unspecified phase)
0.6429 Remote Similarity NPD8610 Approved
0.6364 Remote Similarity NPD1125 Discovery
0.6316 Remote Similarity NPD8982 Approved
0.629 Remote Similarity NPD8971 Approved
0.6267 Remote Similarity NPD3160 Suspended
0.625 Remote Similarity NPD9023 Clinical (unspecified phase)
0.6232 Remote Similarity NPD9233 Phase 3
0.6232 Remote Similarity NPD9231 Phase 3
0.6232 Remote Similarity NPD9232 Phase 2
0.6207 Remote Similarity NPD8850 Approved
0.6207 Remote Similarity NPD8867 Approved
0.6207 Remote Similarity NPD8866 Approved
0.6167 Remote Similarity NPD329 Discontinued
0.6164 Remote Similarity NPD9109 Discontinued
0.6154 Remote Similarity NPD8211 Approved
0.6154 Remote Similarity NPD8210 Phase 3
0.614 Remote Similarity NPD9658 Clinical (unspecified phase)
0.6129 Remote Similarity NPD9419 Clinical (unspecified phase)
0.6049 Remote Similarity NPD7760 Phase 2
0.6049 Remote Similarity NPD7759 Phase 2
0.6034 Remote Similarity NPD8801 Approved
0.6034 Remote Similarity NPD8870 Approved
0.6 Remote Similarity NPD8947 Approved
0.6 Remote Similarity NPD8802 Approved
0.6 Remote Similarity NPD8946 Approved
0.6 Remote Similarity NPD9021 Approved
0.6 Remote Similarity NPD2263 Discontinued
0.6 Remote Similarity NPD8803 Clinical (unspecified phase)
0.6 Remote Similarity NPD8624 Approved
0.5932 Remote Similarity NPD8810 Clinical (unspecified phase)
0.5893 Remote Similarity NPD8609 Approved
0.5875 Remote Similarity NPD4829 Discontinued
0.5862 Remote Similarity NPD573 Clinical (unspecified phase)
0.5844 Remote Similarity NPD4278 Clinical (unspecified phase)
0.5833 Remote Similarity NPD9214 Phase 3
0.5833 Remote Similarity NPD9213 Approved
0.5833 Remote Similarity NPD3724 Clinical (unspecified phase)
0.5833 Remote Similarity NPD8873 Approved
0.5802 Remote Similarity NPD3733 Clinical (unspecified phase)
0.5775 Remote Similarity NPD8868 Approved
0.5738 Remote Similarity NPD9230 Discontinued
0.573 Remote Similarity NPD6428 Approved
0.5714 Remote Similarity NPD6437 Approved
0.5714 Remote Similarity NPD8849 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6438 Approved
0.5694 Remote Similarity NPD322 Phase 1
0.5694 Remote Similarity NPD9452 Clinical (unspecified phase)
0.5692 Remote Similarity NPD9454 Approved
0.569 Remote Similarity NPD8869 Approved
0.5667 Remote Similarity NPD842 Phase 3
0.5667 Remote Similarity NPD8209 Phase 2
0.5667 Remote Similarity NPD8208 Clinical (unspecified phase)
0.5667 Remote Similarity NPD8038 Phase 2
0.5614 Remote Similarity NPD8217 Clinical (unspecified phase)
0.5614 Remote Similarity NPD8215 Approved
0.5614 Remote Similarity NPD8216 Approved
0.5614 Remote Similarity NPD8214 Approved
0.561 Remote Similarity NPD9577 Approved
0.5606 Remote Similarity NPD9425 Approved
0.56 Remote Similarity NPD2256 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