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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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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
4ffl ADP Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4ffl ADPUncharacterized protein / 1.152
4ffr ATPUncharacterized protein / 1.018
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.907
4ffm ADPUncharacterized protein / 0.905
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.890
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.863
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.854
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.851
3wo0 ADPAlanine--anticapsin ligase / 0.838
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.805
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.800
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.788
2hgs ADPGlutathione synthetase 6.3.2.3 0.785
5c1p ADPD-alanine--D-alanine ligase / 0.780
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.774
3wnz ADPAlanine--anticapsin ligase / 0.768
2zdg ADPD-alanine--D-alanine ligase / 0.759
3rv4 ADPBiotin carboxylase 6.3.4.14 0.755
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.755
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.754
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.752
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.749
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.747
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.746
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.739
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.738
4fu0 ADPD-alanine--D-alanine ligase / 0.738
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.737
2p0a ANPSynapsin-3 / 0.734
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.730
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.730
3lla ACPMyosin heavy chain kinase A 2.7.11.7 0.729
1px2 ATPSynapsin-1 / 0.728
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.723
5bpf ADPD-alanine--D-alanine ligase / 0.722
5c1o ANPD-alanine--D-alanine ligase / 0.721
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.720
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.718
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.717
1cm8 ANPMitogen-activated protein kinase 12 / 0.716
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.716
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.715
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.715
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.715
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.712
3r5f ATPD-alanine--D-alanine ligase / 0.710
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.708
2vqd AP2Biotin carboxylase 6.3.4.14 0.708
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.708
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.707
3wo1 ADPAlanine--anticapsin ligase / 0.706
3g8d ADPBiotin carboxylase 6.3.4.14 0.705
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.704
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.702
3tw6 ADPPyruvate carboxylase / 0.701
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.700
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.699
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.698
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.697
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.697
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.696
3g8c ADPBiotin carboxylase 6.3.4.14 0.695
2j9g ADPBiotin carboxylase 6.3.4.14 0.694
5ce3 ADPProtein kinase YopO / 0.694
2wtk ANPSTE20-related kinase adapter protein alpha / 0.690
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.690
5jqw ADPN5-carboxyaminoimidazole ribonucleotide synthase / 0.690
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.689
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.688
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.688
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.688
1m0w ANPGlutathione synthetase 6.3.2.3 0.687
2wq7 FADRE11660p / 0.687
3cvu FADRE11660p / 0.687
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.687
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.686
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.684
5cb4 ACPTubulin tyrosine ligase / 0.684
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.683
3lfz ADPUncharacterized protein MJ1225 / 0.683
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.683
1aux AGSSynapsin-1 / 0.682
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.682
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.681
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.681
2i8c ADPD-alanine--D-alanine ligase / 0.680
4o4f ATPKinase / 0.680
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.679
2ydo ADNAdenosine receptor A2a / 0.679
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.679
5ckw ANPUncharacterized protein / 0.679
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.678
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.677
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.676
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.676
4ysj ADPCalmodulin-like domain protein kinase / 0.676
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.676
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.674
1pk8 ATPSynapsin-1 / 0.674
2pyw ADPMethylthioribose kinase 2.7.1.100 0.674
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.673
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.673
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.672
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.671
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.671
3pff ADPATP-citrate synthase 2.3.3.8 0.671
3krf DSTGeranyl diphosphate synthase large subunit / 0.670
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.669
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.669
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.669
2pui ADPMethylthioribose kinase 2.7.1.100 0.667
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.667
4o4e ATPKinase / 0.667
3bu5 ATPInsulin receptor 2.7.10.1 0.666
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.666
4utd ACPAurora kinase A 2.7.11.1 0.666
1dv2 ATPBiotin carboxylase 6.3.4.14 0.665
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.665
4gyi ADPUncharacterized protein / 0.665
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.663
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.662
4bwa N0BPyrrolysine--tRNA ligase / 0.661
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.661
5iqe GNPBifunctional AAC/APH 2.3.1 0.661
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.660
3thy ADPDNA mismatch repair protein Msh2 / 0.660
4x8l AP5Adenylate kinase / 0.660
1q97 ATPSerine/threonine-protein kinase SKY1 2.7.11.1 0.659
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.659
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.659
4x8o AP5Adenylate kinase / 0.659
5iqa GNPBifunctional AAC/APH 2.3.1 0.659
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.658
2j9g ANPBiotin carboxylase 6.3.4.14 0.658
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.657
4rx6 ATPNitrogen regulatory PII-like protein / 0.657
4uoh ADPNucleoside diphosphate kinase / 0.657
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
2wb2 FADRE11660p / 0.656
3aky AP5Adenylate kinase / 0.656
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.656
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.656
4bw9 ANPPyrrolysine--tRNA ligase / 0.655
4dee ADPAurora kinase A 2.7.11.1 0.655
5ca0 ACPTubulin tyrosine ligase / 0.655
2pun ACPMethylthioribose kinase 2.7.1.100 0.654
5dn3 ATPAurora kinase A 2.7.11.1 0.654
2pul ACPMethylthioribose kinase 2.7.1.100 0.653
3e9i XAHLysine--tRNA ligase 6.1.1.6 0.653
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.653
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.652
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.652
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.652
2olc ADPMethylthioribose kinase 2.7.1.100 0.652
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.652
3dl0 AP5Adenylate kinase / 0.652
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
4mv3 ACPBiotin carboxylase 6.3.4.14 0.652
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.652
5iqd GNPBifunctional AAC/APH 2.3.1 0.652
2i19 1BYFarnesyl pyrophosphate synthase / 0.651
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.651
3tdw GDPGentamicin resistance protein / 0.651
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
4c3r ACPAurora kinase A 2.7.11.1 0.651
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.651
1v3s ATPSignaling protein / 0.650
4n57 ADPAPH(2'')-Id / 0.650
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.650
5iqb GNPBifunctional AAC/APH 2.3.1 0.650