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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
3biv 11U Prothrombin 3.4.21.5

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3biv 11UProthrombin 3.4.21.5 0.912
2zfq 45UProthrombin 3.4.21.5 0.869
2ziq 26UProthrombin 3.4.21.5 0.869
2zhe 13UProthrombin 3.4.21.5 0.861
2zhf 49UProthrombin 3.4.21.5 0.859
3utu 1TSProthrombin 3.4.21.5 0.856
2zi2 24UProthrombin 3.4.21.5 0.852
2znk 31UProthrombin 3.4.21.5 0.847
2zhq 27UProthrombin 3.4.21.5 0.846
3biu 10UProthrombin 3.4.21.5 0.843
2zg0 50UProthrombin 3.4.21.5 0.835
2zfr 46UProthrombin 3.4.21.5 0.830
1ypm RA4Prothrombin 3.4.21.5 0.806
2v3h I25Prothrombin 3.4.21.5 0.804
4bao MVFProthrombin 3.4.21.5 0.803
2zgx 29UProthrombin 3.4.21.5 0.802
2zda 32UProthrombin 3.4.21.5 0.798
4bah MELProthrombin 3.4.21.5 0.798
4bam MM9Prothrombin 3.4.21.5 0.798
4baq M4ZProthrombin 3.4.21.5 0.798
1k22 MELProthrombin 3.4.21.5 0.797
4ban M6SProthrombin 3.4.21.5 0.796
4bak M67Prothrombin 3.4.21.5 0.794
2bdy UNBProthrombin 3.4.21.5 0.792
1ypl RA8Prothrombin 3.4.21.5 0.787
2zhw 12UProthrombin 3.4.21.5 0.787
2gde SN3Prothrombin 3.4.21.5 0.786
2a2x NA9Prothrombin 3.4.21.5 0.778
3hat GLY_VAL_ARG_RNGProthrombin 3.4.21.5 0.778
1k21 IGNProthrombin 3.4.21.5 0.767
4e7r 0NWProthrombin 3.4.21.5 0.757
2cf8 ESHProthrombin 3.4.21.5 0.755
1ghv 120Prothrombin 3.4.21.5 0.751
1c5n ESIProthrombin 3.4.21.5 0.741
1ypj UIBProthrombin 3.4.21.5 0.739
1c4u IH1Prothrombin 3.4.21.5 0.736
2cf9 348Prothrombin 3.4.21.5 0.735
1c4v IH2Prothrombin 3.4.21.5 0.730
1ypg UIRProthrombin 3.4.21.5 0.728
1vzq SHYProthrombin 3.4.21.5 0.723
3v0x ANHCationic trypsin 3.4.21.4 0.722
1ype UIPProthrombin 3.4.21.5 0.721
3plp BBACationic trypsin 3.4.21.4 0.721
1wtg 3BPCoagulation factor VII 3.4.21.21 0.717
4ayy 9MXProthrombin 3.4.21.5 0.717
1d4p BPPProthrombin 3.4.21.5 0.713
1sqt UI3Urokinase-type plasminogen activator 3.4.21.73 0.711
1ypk CCRProthrombin 3.4.21.5 0.710
1lpk CBBCoagulation factor X 3.4.21.6 0.707
1wqv PSMCoagulation factor VII 3.4.21.21 0.705
2cn0 F25Prothrombin 3.4.21.5 0.704
1vja 7INUrokinase-type plasminogen activator 3.4.21.73 0.700
1c1w BAHProthrombin 3.4.21.5 0.694
1ae8 AZLProthrombin 3.4.21.5 0.693
1kts C24Prothrombin 3.4.21.5 0.691
1o2g 696Prothrombin 3.4.21.5 0.689
1o5g CR9Prothrombin 3.4.21.5 0.687
1lqd CMICoagulation factor X 3.4.21.6 0.683
2v3o I26Prothrombin 3.4.21.5 0.682
1o0d 163Prothrombin 3.4.21.5 0.681
4ax9 N5NProthrombin 3.4.21.5 0.681
1owi 426Urokinase-type plasminogen activator 3.4.21.73 0.679
1oyt FSNProthrombin 3.4.21.5 0.679
4az2 9MUProthrombin 3.4.21.5 0.679
4fud 6UPUrokinase-type plasminogen activator 3.4.21.73 0.676
1afe ALZProthrombin 3.4.21.5 0.675
1owe 675Urokinase-type plasminogen activator 3.4.21.73 0.674
1gj5 130Prothrombin 3.4.21.5 0.669
4ayv 9MQProthrombin 3.4.21.5 0.667
1jwt BLIProthrombin 3.4.21.5 0.664
1uvs I11Prothrombin 3.4.21.5 0.663
1drt PCVClavaminate synthase 1 1.14.11.21 0.660
1ny2 ARG_PRO_PRO_GLYProthrombin 3.4.21.5 0.659
4ne0 ZZUHydroxylase / 0.658
4djw 0KPBeta-secretase 1 3.4.23.46 0.657
1vaf ARRNitric oxide synthase, inducible 1.14.13.39 0.656
4dju 0KKBeta-secretase 1 3.4.23.46 0.655
1nzq 162Prothrombin 3.4.21.5 0.654
2bok 784Coagulation factor X 3.4.21.6 0.653
2c4f GILCoagulation factor VII 3.4.21.21 0.653
3qdz PRO_ALA_PRO_ARGProthrombin 3.4.21.5 0.653
4azy 7F3Beta-secretase 1 3.4.23.46 0.651
1d9i 00PProthrombin 3.4.21.5 0.650
1t4v 14AProthrombin 3.4.21.5 0.650