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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
2zfr 46U Prothrombin 3.4.21.5

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zfr 46UProthrombin 3.4.21.5 0.921
2zfq 45UProthrombin 3.4.21.5 0.897
2zi2 24UProthrombin 3.4.21.5 0.897
2zhq 27UProthrombin 3.4.21.5 0.892
2znk 31UProthrombin 3.4.21.5 0.889
2zhf 49UProthrombin 3.4.21.5 0.886
2zg0 50UProthrombin 3.4.21.5 0.878
2zgx 29UProthrombin 3.4.21.5 0.871
3utu 1TSProthrombin 3.4.21.5 0.868
2zda 32UProthrombin 3.4.21.5 0.866
1ypl RA8Prothrombin 3.4.21.5 0.849
2ziq 26UProthrombin 3.4.21.5 0.841
4bao MVFProthrombin 3.4.21.5 0.832
1k22 MELProthrombin 3.4.21.5 0.831
1ypm RA4Prothrombin 3.4.21.5 0.831
2zhe 13UProthrombin 3.4.21.5 0.831
3biv 11UProthrombin 3.4.21.5 0.831
4bah MELProthrombin 3.4.21.5 0.831
4bam MM9Prothrombin 3.4.21.5 0.831
4ban M6SProthrombin 3.4.21.5 0.828
4bak M67Prothrombin 3.4.21.5 0.826
4baq M4ZProthrombin 3.4.21.5 0.813
2anm CDOProthrombin 3.4.21.5 0.803
3biu 10UProthrombin 3.4.21.5 0.783
2v3h I25Prothrombin 3.4.21.5 0.776
2bdy UNBProthrombin 3.4.21.5 0.773
1riw OSCProthrombin 3.4.21.5 0.771
3hat GLY_VAL_ARG_RNGProthrombin 3.4.21.5 0.765
2a2x NA9Prothrombin 3.4.21.5 0.762
1c4u IH1Prothrombin 3.4.21.5 0.759
2v3o I26Prothrombin 3.4.21.5 0.750
1afe ALZProthrombin 3.4.21.5 0.746
1ype UIPProthrombin 3.4.21.5 0.746
4ayy 9MXProthrombin 3.4.21.5 0.745
1g7u PEP2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.744
4e5i 0N9Polymerase acidic protein / 0.744
2gde SN3Prothrombin 3.4.21.5 0.743
1c4v IH2Prothrombin 3.4.21.5 0.737
1k21 IGNProthrombin 3.4.21.5 0.737
2zhw 12UProthrombin 3.4.21.5 0.736
2cf9 348Prothrombin 3.4.21.5 0.734
2cn0 F25Prothrombin 3.4.21.5 0.734
1oyt FSNProthrombin 3.4.21.5 0.730
1c5n ESIProthrombin 3.4.21.5 0.727
1ypj UIBProthrombin 3.4.21.5 0.724
1wtg 3BPCoagulation factor VII 3.4.21.21 0.722
2cf8 ESHProthrombin 3.4.21.5 0.720
3plp BBACationic trypsin 3.4.21.4 0.719
1ypk CCRProthrombin 3.4.21.5 0.718
1lpk CBBCoagulation factor X 3.4.21.6 0.713
1d4p BPPProthrombin 3.4.21.5 0.711
1ghv 120Prothrombin 3.4.21.5 0.710
4ayv 9MQProthrombin 3.4.21.5 0.708
4ax9 N5NProthrombin 3.4.21.5 0.707
1vja 7INUrokinase-type plasminogen activator 3.4.21.73 0.703
1ypg UIRProthrombin 3.4.21.5 0.703
1zsk 421Coagulation factor XI 3.4.21.27 0.703
1uvs I11Prothrombin 3.4.21.5 0.699
5cmx 0G6Prothrombin 3.4.21.5 0.698
2zff 53UProthrombin 3.4.21.5 0.695
2zdv 37UProthrombin 3.4.21.5 0.693
4az2 9MUProthrombin 3.4.21.5 0.693
3qwc 98PProthrombin 3.4.21.5 0.690
3qdz PRO_ALA_PRO_ARGProthrombin 3.4.21.5 0.685
4e7r 0NWProthrombin 3.4.21.5 0.685
2zfp 19UProthrombin 3.4.21.5 0.684
1jwt BLIProthrombin 3.4.21.5 0.679
3eq0 2TSProthrombin 3.4.21.5 0.673
3f68 91UProthrombin 3.4.21.5 0.673
2bok 784Coagulation factor X 3.4.21.6 0.671
3dux 64UProthrombin 3.4.21.5 0.671
1ta2 176Prothrombin 3.4.21.5 0.670
1zrb 062Prothrombin 3.4.21.5 0.670
1ae8 AZLProthrombin 3.4.21.5 0.667
3qtv 06PProthrombin 3.4.21.5 0.665
1c1w BAHProthrombin 3.4.21.5 0.664
2zp0 PI0Coagulation factor VII 3.4.21.21 0.664
1t4u 81AProthrombin 3.4.21.5 0.663
2zc9 22UProthrombin 3.4.21.5 0.661
3p17 99PProthrombin 3.4.21.5 0.661
1c1u BAIProthrombin 3.4.21.5 0.660
1o5g CR9Prothrombin 3.4.21.5 0.660
2c4f GILCoagulation factor VII 3.4.21.21 0.659
3qto 10PProthrombin 3.4.21.5 0.658
4djw 0KPBeta-secretase 1 3.4.23.46 0.657
3dhk 23UProthrombin 3.4.21.5 0.656
4djy 0KRBeta-secretase 1 3.4.23.46 0.656
4jpc 1M6Beta-secretase 1 3.4.23.46 0.656
1o2g 696Prothrombin 3.4.21.5 0.654
3l5e BDWBeta-secretase 1 3.4.23.46 0.654
2zgb 21UProthrombin 3.4.21.5 0.653
4acx S8ZBeta-secretase 1 3.4.23.46 0.652
4b0q GMFBeta-secretase 1 3.4.23.46 0.652