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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
4i0b CMP cAMP-activated global transcriptional regulator CRP

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4i0b CMPcAMP-activated global transcriptional regulator CRP / 1.000
3ryp CMPcAMP-activated global transcriptional regulator CRP / 0.921
4hzf CMPcAMP-activated global transcriptional regulator CRP / 0.920
4ft8 CMPcAMP-activated global transcriptional regulator CRP / 0.919
3kcc CMPcAMP-activated global transcriptional regulator CRP / 0.907
4i09 CMPcAMP-activated global transcriptional regulator CRP / 0.905
3qop CMPcAMP-activated global transcriptional regulator CRP / 0.904
1i5z CMPcAMP-activated global transcriptional regulator CRP / 0.903
2cgp CMPcAMP-activated global transcriptional regulator CRP / 0.901
4i0a CMPcAMP-activated global transcriptional regulator CRP / 0.891
2oz6 CMPCyclic AMP receptor-like protein / 0.889
3rou CMPcAMP-activated global transcriptional regulator CRP / 0.885
4i01 CMPcAMP-activated global transcriptional regulator CRP / 0.883
4i02 CMPcAMP-activated global transcriptional regulator CRP / 0.881
1g6n CMPcAMP-activated global transcriptional regulator CRP / 0.880
1zrd CMPcAMP-activated global transcriptional regulator CRP / 0.870
4r8h SP1cAMP-activated global transcriptional regulator CRP / 0.866
3rpq CMPcAMP-activated global transcriptional regulator CRP / 0.863
1hw5 CMPcAMP-activated global transcriptional regulator CRP / 0.861
1i6x CMPcAMP-activated global transcriptional regulator CRP / 0.859
3ryr CMPcAMP-activated global transcriptional regulator CRP / 0.857
3n4m CMPcAMP-activated global transcriptional regulator CRP / 0.846
2ptm CMPHyperpolarization-activated (Ih) channel / 0.814
1vp6 CMPCyclic nucleotide-gated potassium channel mll3241 / 0.812
1zrc CMPcAMP-activated global transcriptional regulator CRP / 0.801
2gzw CMPcAMP-activated global transcriptional regulator CRP / 0.795
5c6c CMPcGMP-dependent protein kinase 2 2.7.11.12 0.787
1q43 CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / 0.786
4d7t CMPUncharacterized protein / 0.784
3ocp CMPcGMP-dependent protein kinase 1 2.7.11.12 0.774
4ku7 PCGcGMP-dependent protein kinase 1 2.7.11.12 0.763
3bpz CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / 0.759
3ogj CMPcGMP-dependent protein kinase 1 2.7.11.12 0.755
3shr CMPcGMP-dependent protein kinase 1 2.7.11.12 0.752
3otf CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / 0.748
4hbn CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / 0.747
3u10 CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / 0.745
4qx5 CMPcGMP-dependent protein kinase 1 2.7.11.12 0.741
3u0z CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 / 0.740
1rgs CMPcAMP-dependent protein kinase type I-alpha regulatory subunit / 0.727
4mgk CMPRap guanine nucleotide exchange factor 4 / 0.726
3rdi CMPcAMP-activated global transcriptional regulator CRP / 0.725
1q5o CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / 0.724
3u11 CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / 0.724
3i59 N6RCRP-like cAMP-activated global transcriptional regulator / 0.722
1cx4 CMPcAMP-dependent protein kinase type II-beta regulatory subunit / 0.718
4ev0 CMPCyclic AMP receptor protein / 0.712
1ne6 SP1cAMP-dependent protein kinase type I-alpha regulatory subunit / 0.710
4d7s PCGUncharacterized protein / 0.709
1q3e PCGPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / 0.708
3cl1 PCGCyclic nucleotide-gated potassium channel mll3241 / 0.708
4n9i PCGCatabolite expression activator / 0.708
5c8w PCGcGMP-dependent protein kinase 2 2.7.11.12 0.707
1ne4 RP1cAMP-dependent protein kinase type I-alpha regulatory subunit / 0.705
2k0g CMPCyclic nucleotide-gated potassium channel mll3241 / 0.704
4z07 PCGcGMP-dependent protein kinase 1 2.7.11.12 0.704
1cgp CMPcAMP-activated global transcriptional regulator CRP / 0.702
3i59 N6SCRP-like cAMP-activated global transcriptional regulator / 0.700
4jv4 1ORcAMP-dependent protein kinase type I-alpha regulatory subunit / 0.697
4jva 1ORcAMP-dependent protein kinase type II-beta regulatory subunit / 0.695
3plq RP2cAMP-dependent protein kinase type I-alpha regulatory subunit / 0.690
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.681
1nhk CMPNucleoside diphosphate kinase 2.7.4.6 0.678
2p0a ANPSynapsin-3 / 0.674
3of1 CMPcAMP-dependent protein kinase regulatory subunit / 0.672
1ruo CMPcAMP-activated global transcriptional regulator CRP / 0.669
3r6s CMPCRP-like cAMP-activated global transcriptional regulator / 0.667
1mjh ATPUniversal stress protein MJ0577 / 0.664
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.664
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.663
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.663
3od0 PCGcGMP-dependent protein kinase 1 2.7.11.12 0.662
4ffm ADPUncharacterized protein / 0.662
4hr2 ADPNucleoside diphosphate kinase / 0.660
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.660
2eka SAHDiphthine synthase / 0.659
1kor ANPArgininosuccinate synthase / 0.658
2dxe GDPNucleoside diphosphate kinase 2.7.4.6 0.657
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.656
2ydo ADNAdenosine receptor A2a / 0.655
2z6r SAHDiphthine synthase / 0.655
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.655
3wnz ADPAlanine--anticapsin ligase / 0.655
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.655
2e15 SAHDiphthine synthase / 0.654
2e7r SAHDiphthine synthase / 0.654
4fkx CDPNucleoside diphosphate kinase / 0.654
2dxv SAHDiphthine synthase / 0.653
2e07 SAHDiphthine synthase / 0.653
2egl SAHDiphthine synthase / 0.653
3ab8 ATPUncharacterized protein / 0.653
3dge ADPSensor histidine kinase / 0.653
4yb7 ATPATP phosphoribosyltransferase / 0.652
2z08 ATPUniversal stress protein family / 0.651
4uoh ADPNucleoside diphosphate kinase / 0.651
4wud ANPDNA gyrase subunit B / 0.651
2owk SAHDiphthine synthase / 0.650
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.650