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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
1vp6 CMP Cyclic nucleotide-gated potassium channel mll3241

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1vp6 CMPCyclic nucleotide-gated potassium channel mll3241 / 0.968
3cl1 PCGCyclic nucleotide-gated potassium channel mll3241 / 0.865
3otf CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / 0.859
4qx5 CMPcGMP-dependent protein kinase 1 2.7.11.12 0.842
2ptm CMPHyperpolarization-activated (Ih) channel / 0.835
4ft8 CMPcAMP-activated global transcriptional regulator CRP / 0.827
4hzf CMPcAMP-activated global transcriptional regulator CRP / 0.826
4i02 CMPcAMP-activated global transcriptional regulator CRP / 0.825
3rou CMPcAMP-activated global transcriptional regulator CRP / 0.821
3ryp CMPcAMP-activated global transcriptional regulator CRP / 0.821
3u11 CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / 0.816
3bpz CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / 0.815
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.812
4d7t CMPUncharacterized protein / 0.809
1q43 CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / 0.804
4hbn CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 / 0.802
4ku7 PCGcGMP-dependent protein kinase 1 2.7.11.12 0.801
2cgp CMPcAMP-activated global transcriptional regulator CRP / 0.793
1i5z CMPcAMP-activated global transcriptional regulator CRP / 0.791
1rgs CMPcAMP-dependent protein kinase type I-alpha regulatory subunit / 0.791
2oz6 CMPCyclic AMP receptor-like protein / 0.791
4ev0 CMPCyclic AMP receptor protein / 0.788
3rpq CMPcAMP-activated global transcriptional regulator CRP / 0.786
3ryr CMPcAMP-activated global transcriptional regulator CRP / 0.784
4i0a CMPcAMP-activated global transcriptional regulator CRP / 0.784
4jva 1ORcAMP-dependent protein kinase type II-beta regulatory subunit / 0.780
3ocp CMPcGMP-dependent protein kinase 1 2.7.11.12 0.777
3qop CMPcAMP-activated global transcriptional regulator CRP / 0.774
3n4m CMPcAMP-activated global transcriptional regulator CRP / 0.773
4r8h SP1cAMP-activated global transcriptional regulator CRP / 0.772
4z07 PCGcGMP-dependent protein kinase 1 2.7.11.12 0.772
1cx4 CMPcAMP-dependent protein kinase type II-beta regulatory subunit / 0.771
3u10 CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / 0.771
4i09 CMPcAMP-activated global transcriptional regulator CRP / 0.771
1q3e PCGPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / 0.769
3kcc CMPcAMP-activated global transcriptional regulator CRP / 0.767
1i6x CMPcAMP-activated global transcriptional regulator CRP / 0.763
1q5o CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / 0.755
4mgk CMPRap guanine nucleotide exchange factor 4 / 0.755
5c6c CMPcGMP-dependent protein kinase 2 2.7.11.12 0.752
1zrd CMPcAMP-activated global transcriptional regulator CRP / 0.750
3u0z CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 / 0.747
4d7s PCGUncharacterized protein / 0.739
3rdi CMPcAMP-activated global transcriptional regulator CRP / 0.737
1ne6 SP1cAMP-dependent protein kinase type I-alpha regulatory subunit / 0.735
1g6n CMPcAMP-activated global transcriptional regulator CRP / 0.733
2gzw CMPcAMP-activated global transcriptional regulator CRP / 0.732
3od0 PCGcGMP-dependent protein kinase 1 2.7.11.12 0.729
3r6s CMPCRP-like cAMP-activated global transcriptional regulator / 0.729
3of1 CMPcAMP-dependent protein kinase regulatory subunit / 0.727
3shr CMPcGMP-dependent protein kinase 1 2.7.11.12 0.725
2k0g CMPCyclic nucleotide-gated potassium channel mll3241 / 0.724
4i01 CMPcAMP-activated global transcriptional regulator CRP / 0.723
1ne4 RP1cAMP-dependent protein kinase type I-alpha regulatory subunit / 0.721
1zrc CMPcAMP-activated global transcriptional regulator CRP / 0.711
1hw5 CMPcAMP-activated global transcriptional regulator CRP / 0.704
4kg1 PCGDiguanylate cyclase / 0.701
3i59 N6RCRP-like cAMP-activated global transcriptional regulator / 0.700
3plq RP2cAMP-dependent protein kinase type I-alpha regulatory subunit / 0.696
1rl3 PCGcAMP-dependent protein kinase type I-alpha regulatory subunit / 0.689
2p0a ANPSynapsin-3 / 0.685
2dxe GDPNucleoside diphosphate kinase 2.7.4.6 0.683
4n9i PCGCatabolite expression activator / 0.681
5c8w PCGcGMP-dependent protein kinase 2 2.7.11.12 0.680
4hr2 ADPNucleoside diphosphate kinase / 0.674
3bbf GDPNucleoside diphosphate kinase B 2.7.4.6 0.673
4fkx CDPNucleoside diphosphate kinase / 0.672
4jv4 1ORcAMP-dependent protein kinase type I-alpha regulatory subunit / 0.672
3i59 N6SCRP-like cAMP-activated global transcriptional regulator / 0.668
3ogj CMPcGMP-dependent protein kinase 1 2.7.11.12 0.667
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.664
2hve ADPNucleoside diphosphate kinase A 2.7.4.6 0.662
1nue GDPNucleoside diphosphate kinase B 2.7.4.6 0.659
4uoh ADPNucleoside diphosphate kinase / 0.657
1ruo CMPcAMP-activated global transcriptional regulator CRP / 0.656
2hvd ADPNucleoside diphosphate kinase A 2.7.4.6 0.655
2dxf GNPNucleoside diphosphate kinase 2.7.4.6 0.653
4mgi CMPRap guanine nucleotide exchange factor 4 / 0.653
4wbd ADPPutative cysteine ligase BshC / 0.652
4uof DATNucleoside diphosphate kinase / 0.651