Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
5c1p ADP D-alanine--D-alanine ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5c1p ADPD-alanine--D-alanine ligase / 1.063
5c1o ANPD-alanine--D-alanine ligase / 0.894
5bpf ADPD-alanine--D-alanine ligase / 0.864
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.833
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.783
4ffl ADPUncharacterized protein / 0.780
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.778
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.754
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.754
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.751
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.750
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.750
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.749
4fu0 ADPD-alanine--D-alanine ligase / 0.748
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.740
3tw6 ADPPyruvate carboxylase / 0.734
4ffm ADPUncharacterized protein / 0.734
4ffr ATPUncharacterized protein / 0.733
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.728
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.727
1px2 ATPSynapsin-1 / 0.722
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.722
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.721
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.717
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.714
5jqw ADPN5-carboxyaminoimidazole ribonucleotide synthase / 0.710
3wo0 ADPAlanine--anticapsin ligase / 0.708
2p0a ANPSynapsin-3 / 0.706
3g8d ADPBiotin carboxylase 6.3.4.14 0.706
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.704
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.703
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.698
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.697
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.696
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.694
3pff ADPATP-citrate synthase 2.3.3.8 0.691
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.682
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.680
1aux AGSSynapsin-1 / 0.676
2zdg ADPD-alanine--D-alanine ligase / 0.675
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.675
5ifi PRXAcetyl-coenzyme A synthetase / 0.672
2p2j PRXAcetyl-coenzyme A synthetase / 0.671
4qny ANPMitogen activated protein kinase, putative / 0.671
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.670
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.670
4s26 SAHPhosphomethylpyrimidine synthase, chloroplastic 4.1.99.17 0.669
4mv1 ADPBiotin carboxylase 6.3.4.14 0.668
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.666
2ilv C5PAlpha-2,3/2,6-sialyltransferase/sialidase / 0.664
4ma5 ANPN5-carboxyaminoimidazole ribonucleotide synthase / 0.664
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.663
3r5f ATPD-alanine--D-alanine ligase / 0.663
2j9g ANPBiotin carboxylase 6.3.4.14 0.662
2ha8 SAHProbable methyltransferase TARBP1 / 0.661
4cng SAHSpoU rRNA methylase / 0.660
1bxr ANPCarbamoyl-phosphate synthase large chain / 0.659
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.659
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.658
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.658
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.657
2d1s SLULuciferin 4-monooxygenase 1.13.12.7 0.656
4jwh SAHtRNA (guanine(9)-N1)-methyltransferase / 0.654
4jwj SAHtRNA (guanine(9)-N1)-methyltransferase / 0.653
1m0w ANPGlutathione synthetase 6.3.2.3 0.652
1pk8 ATPSynapsin-1 / 0.652
2z08 ATPUniversal stress protein family / 0.652
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.652
4lrj ANPUncharacterized protein / 0.652
1qrt ATPGlutamine--tRNA ligase 6.1.1.18 0.651
2c2a ADPSensor histidine kinase / 0.651
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.651
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.651
4u0o MTALipoyl synthase 2 / 0.651
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.650