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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
4c5b ADP D-alanine--D-alanine ligase B 6.3.2.4

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 1.266
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 1.185
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.934
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.921
4ffl ADPUncharacterized protein / 0.907
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.889
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.880
4ffr ATPUncharacterized protein / 0.879
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.874
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.857
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.848
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.847
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.844
2p0a ANPSynapsin-3 / 0.840
5c1p ADPD-alanine--D-alanine ligase / 0.833
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.828
3wnz ADPAlanine--anticapsin ligase / 0.827
3wo0 ADPAlanine--anticapsin ligase / 0.806
4fu0 ADPD-alanine--D-alanine ligase / 0.802
2hgs ADPGlutathione synthetase 6.3.2.3 0.799
5bpf ADPD-alanine--D-alanine ligase / 0.797
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.787
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.787
1px2 ATPSynapsin-1 / 0.786
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.781
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.780
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.780
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.780
3tw6 ADPPyruvate carboxylase / 0.779
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.776
4ffm ADPUncharacterized protein / 0.774
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.772
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.771
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.763
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.763
5c1o ANPD-alanine--D-alanine ligase / 0.762
3rv4 ADPBiotin carboxylase 6.3.4.14 0.761
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.759
4qny ANPMitogen activated protein kinase, putative / 0.759
4xlv ACPInsulin receptor 2.7.10.1 0.758
1m0w ANPGlutathione synthetase 6.3.2.3 0.756
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.756
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.755
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.752
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.751
4xw6 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.751
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.750
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.750
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.749
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.748
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.748
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.744
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.742
3bu5 ATPInsulin receptor 2.7.10.1 0.742
1jdb ADPCarbamoyl-phosphate synthase large chain / 0.740
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.740
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.740
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.740
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.731
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.729
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.727
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.727
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.726
3cvu FADRE11660p / 0.725
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.725
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.724
5ce3 ADPProtein kinase YopO / 0.723
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.722
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.721
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.721
2wq7 FADRE11660p / 0.720
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.719
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.719
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.718
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.718
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.717
2pyw ADPMethylthioribose kinase 2.7.1.100 0.717
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.717
1iah ADPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.716
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.714
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.714
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.713
2zdg ADPD-alanine--D-alanine ligase / 0.712
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.711
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.711
1bxr ANPCarbamoyl-phosphate synthase large chain / 0.710
3r5f ATPD-alanine--D-alanine ligase / 0.710
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.710
1q24 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
2w4k ADPDeath-associated protein kinase 1 2.7.11.1 0.709
3pff ADPATP-citrate synthase 2.3.3.8 0.708
4nif ANPMitogen-activated protein kinase 1 2.7.11.24 0.708
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.707
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.707
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.706
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.704
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.703
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.703
4ceg ADPAurora kinase A 2.7.11.1 0.703
4h3q ANPMitogen-activated protein kinase 1 2.7.11.24 0.702
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.701
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.701
3cr3 ADPPTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL 2.7 0.701
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.701
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.700
2vqd AP2Biotin carboxylase 6.3.4.14 0.697
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.697
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.697
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.696
4dee ADPAurora kinase A 2.7.11.1 0.696
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.695
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.694
1w2d ADPInositol-trisphosphate 3-kinase A 2.7.1.127 0.694
3g51 ANPRibosomal protein S6 kinase alpha-3 2.7.11.1 0.693
4o4e ATPKinase / 0.692
1q97 ATPSerine/threonine-protein kinase SKY1 2.7.11.1 0.691
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.691
3nsz ANPCasein kinase II subunit alpha 2.7.11.1 0.691
4uxx ACPDiacylglycerol kinase 2.7.1.107 0.691
1pk8 ATPSynapsin-1 / 0.690
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.689
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.689
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.689
4axf ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.689
4o4f ATPKinase / 0.689
5iqb GNPBifunctional AAC/APH 2.3.1 0.689
4wh2 ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.688
3wo1 ADPAlanine--anticapsin ligase / 0.687
5dr2 ATPAurora kinase A 2.7.11.1 0.687
4ix5 ANPUncharacterized protein / 0.685
3cly ACPFibroblast growth factor receptor 2 / 0.684
4ysj ADPCalmodulin-like domain protein kinase / 0.684
5dn3 ATPAurora kinase A 2.7.11.1 0.684
2pun ACPMethylthioribose kinase 2.7.1.100 0.683
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.683
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.683
1mru AGSSerine/threonine-protein kinase PknB 2.7.11.1 0.682
2yw2 ATPPhosphoribosylamine--glycine ligase / 0.682
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.682
3lmi ATPMyosin heavy chain kinase A 2.7.11.7 0.681
4bwa N0BPyrrolysine--tRNA ligase / 0.681
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.680
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.680
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.680
4axd ANPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.679
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.679
1aux AGSSynapsin-1 / 0.678
3cvy FADRE11660p / 0.678
5jqw ADPN5-carboxyaminoimidazole ribonucleotide synthase / 0.678
1ia9 ANPTransient receptor potential cation channel subfamily M member 7 2.7.11.1 0.677
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.677
3zu0 A12NAD 5'-nucleotidase 3.1.3.5 0.677
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.677
1g6n CMPcAMP-activated global transcriptional regulator CRP / 0.676
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.676
1jnk ANPMitogen-activated protein kinase 10 2.7.11.24 0.676
2ydo ADNAdenosine receptor A2a / 0.676
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.676
4s1h ADPPyridoxal kinase, putative / 0.676
1ir3 ANPInsulin receptor 2.7.10.1 0.674
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.674
3a5z KAAElongation factor P--(R)-beta-lysine ligase / 0.674
4jqe ANPCasein kinase II subunit alpha 2.7.11.1 0.674
4ork GDPBifunctional AAC/APH 2.3.1 0.674
5drd ATPAurora kinase A 2.7.11.1 0.674
1kh3 ANPArgininosuccinate synthase / 0.673
4lv7 ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.673
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.672
4r8h SP1cAMP-activated global transcriptional regulator CRP / 0.672
5byl GCPBifunctional AAC/APH 2.3.1 0.672
2gzw CMPcAMP-activated global transcriptional regulator CRP / 0.671
2wq6 FADRE11660p / 0.671
2x86 ADPADP-L-glycero-D-manno-heptose-6-epimerase / 0.671
3gu4 ANPDeath-associated protein kinase 1 2.7.11.1 0.671
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.671
1j1b ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.670
2b56 UTPRNA editing complex protein MP57 / 0.670
3c4w ATPRhodopsin kinase / 0.670
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.670
3kcc CMPcAMP-activated global transcriptional regulator CRP / 0.670
4cnf MTASpoU rRNA methylase / 0.670
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.670
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.670
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.669
1day GNPCasein kinase II subunit alpha 2.7.11.1 0.668
2rio ADPSerine/threonine-protein kinase/endoribonuclease IRE1 2.7.11.1 0.668
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.668
3a5y KAAElongation factor P--(R)-beta-lysine ligase / 0.668
3c4z ADPRhodopsin kinase / 0.668
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.668
3t8o ATPRhodopsin kinase / 0.667
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.667
4ix6 ADPUncharacterized protein / 0.667
4jlp ADPAdenylate kinase / 0.667
4x8o AP5Adenylate kinase / 0.667
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.667
1wc0 APCAdenylate cyclase / 0.666
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.666
3tdw GDPGentamicin resistance protein / 0.666
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.666
4g37 SLULuciferin 4-monooxygenase 1.13.12.7 0.666
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.665
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
1nj5 P5AProline--tRNA ligase / 0.665
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.665
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.665
4c3r ACPAurora kinase A 2.7.11.1 0.665
4cng SAHSpoU rRNA methylase / 0.665
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.665
4ux9 ANPMitogen-activated protein kinase 8 2.7.11.24 0.665
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.664
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.664
3krf DSTGeranyl diphosphate synthase large subunit / 0.664
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.664
4ehy ADPTetraacyldisaccharide 4'-kinase / 0.664
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.664
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.664
1cm8 ANPMitogen-activated protein kinase 12 / 0.663
3dqw AGSProto-oncogene tyrosine-protein kinase Src 2.7.10.2 0.663
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.663
2j9g ANPBiotin carboxylase 6.3.4.14 0.662
3c50 ADPRhodopsin kinase / 0.662
3hpr AP5Adenylate kinase / 0.662
5dt3 ATPAurora kinase A 2.7.11.1 0.662
1v3s ATPSignaling protein / 0.661
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.661
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.661
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.661
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.660
4oxi GAPEnterobactin synthetase component F-related protein / 0.660
5la6 ACPTubulin tyrosine ligase / 0.660
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.659
1s4d SAHUroporphyrinogen-III C-methyltransferase 2.1.1.107 0.658
3ies M24Luciferin 4-monooxygenase 1.13.12.7 0.658
4ma5 ANPN5-carboxyaminoimidazole ribonucleotide synthase / 0.658
1kor ANPArgininosuccinate synthase / 0.657
2pml ANPUncharacterized protein / 0.657
3ibq ATPPyridoxal kinase / 0.657
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.657
4jl8 ADPAdenylate kinase / 0.657
5iqh GNPBifunctional AAC/APH 2.3.1 0.657
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.656
2aky AP5Adenylate kinase / 0.656
3t7v SAM3-methylornithine synthase / 0.656
3ufg ATPGlycine--tRNA ligase alpha subunit / 0.656
4bl1 ANPMaternal embryonic leucine zipper kinase 2.7.11.1 0.656
4rx6 ATPNitrogen regulatory PII-like protein / 0.656
5cb4 ACPTubulin tyrosine ligase / 0.656
5dnr ATPAurora kinase A 2.7.11.1 0.656
1dv2 ATPBiotin carboxylase 6.3.4.14 0.655
1pg3 PRXAcetyl-coenzyme A synthetase / 0.655
2ijm ADPFocal adhesion kinase 1 2.7.10.2 0.655
2acx ANPG protein-coupled receptor kinase 6 2.7.11.16 0.654
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.654
2w5a ADPSerine/threonine-protein kinase Nek2 2.7.11.1 0.654
3ryp CMPcAMP-activated global transcriptional regulator CRP / 0.654
5cns CDPRibonucleoside-diphosphate reductase 1 subunit alpha 1.17.4.1 0.654
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.653
1s16 ANPDNA topoisomerase 4 subunit B / 0.653
2aj4 ANPGalactokinase 2.7.1.6 0.653
3ung ADPCRISPR system Cmr subunit Cmr2 / 0.653
4azw ATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.653
4q5h ANPProtein kinase OspG 2.7 0.653
5eg3 ACPFibroblast growth factor receptor 2 / 0.653
1rfu ADPPyridoxal kinase 2.7.1.35 0.652
1rgs CMPcAMP-dependent protein kinase type I-alpha regulatory subunit / 0.652
4hzf CMPcAMP-activated global transcriptional regulator CRP / 0.652
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.652
1kh2 ATPArgininosuccinate synthase / 0.651
3rl3 5GPMetallophosphoesterase MPPED2 3.1 0.651
3s87 ADPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.651
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.651
4pjj ADPUnconventional myosin-VI / 0.651
4xfj ANPArgininosuccinate synthase / 0.651
1mx0 ANPType 2 DNA topoisomerase 6 subunit B / 0.650