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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
4bak M67 Prothrombin 3.4.21.5

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4bak M67Prothrombin 3.4.21.5 1.250
4bah MELProthrombin 3.4.21.5 1.141
4bao MVFProthrombin 3.4.21.5 1.140
4ban M6SProthrombin 3.4.21.5 1.139
4baq M4ZProthrombin 3.4.21.5 1.122
1k22 MELProthrombin 3.4.21.5 1.120
4bam MM9Prothrombin 3.4.21.5 1.058
2znk 31UProthrombin 3.4.21.5 0.950
2zg0 50UProthrombin 3.4.21.5 0.916
2zfq 45UProthrombin 3.4.21.5 0.901
2a2x NA9Prothrombin 3.4.21.5 0.880
2ziq 26UProthrombin 3.4.21.5 0.877
2zi2 24UProthrombin 3.4.21.5 0.873
1ypm RA4Prothrombin 3.4.21.5 0.869
2zhf 49UProthrombin 3.4.21.5 0.860
1ta6 177Prothrombin 3.4.21.5 0.855
2zda 32UProthrombin 3.4.21.5 0.834
3utu 1TSProthrombin 3.4.21.5 0.830
1nt1 T76Prothrombin 3.4.21.5 0.827
2zfr 46UProthrombin 3.4.21.5 0.826
2bdy UNBProthrombin 3.4.21.5 0.805
1nzq 162Prothrombin 3.4.21.5 0.802
2anm CDOProthrombin 3.4.21.5 0.802
2zhq 27UProthrombin 3.4.21.5 0.802
1wqv PSMCoagulation factor VII 3.4.21.21 0.800
3biv 11UProthrombin 3.4.21.5 0.793
1ype UIPProthrombin 3.4.21.5 0.792
3biu 10UProthrombin 3.4.21.5 0.791
1lpk CBBCoagulation factor X 3.4.21.6 0.784
2zhw 12UProthrombin 3.4.21.5 0.783
2v3o I26Prothrombin 3.4.21.5 0.782
3plp BBACationic trypsin 3.4.21.4 0.778
2v3h I25Prothrombin 3.4.21.5 0.769
1c4v IH2Prothrombin 3.4.21.5 0.767
1ypk CCRProthrombin 3.4.21.5 0.764
2cf8 ESHProthrombin 3.4.21.5 0.762
4ayy 9MXProthrombin 3.4.21.5 0.762
1o0d 163Prothrombin 3.4.21.5 0.758
1ypl RA8Prothrombin 3.4.21.5 0.756
1k21 IGNProthrombin 3.4.21.5 0.753
2gde SN3Prothrombin 3.4.21.5 0.753
2zgx 29UProthrombin 3.4.21.5 0.749
3p17 99PProthrombin 3.4.21.5 0.747
1riw OSCProthrombin 3.4.21.5 0.745
1c4u IH1Prothrombin 3.4.21.5 0.740
3v0x ANHCationic trypsin 3.4.21.4 0.739
2zgb 21UProthrombin 3.4.21.5 0.734
1c5n ESIProthrombin 3.4.21.5 0.728
1ae8 AZLProthrombin 3.4.21.5 0.725
1ghv 120Prothrombin 3.4.21.5 0.725
1wtg 3BPCoagulation factor VII 3.4.21.21 0.725
2cf9 348Prothrombin 3.4.21.5 0.725
5cmx 0G6Prothrombin 3.4.21.5 0.725
2cn0 F25Prothrombin 3.4.21.5 0.724
3c1k T15Prothrombin 3.4.21.5 0.724
4e7r 0NWProthrombin 3.4.21.5 0.724
7kme ACE_0BN_CHG_PRRProthrombin 3.4.21.5 0.724
1ypj UIBProthrombin 3.4.21.5 0.723
4ayv 9MQProthrombin 3.4.21.5 0.723
3qwc 98PProthrombin 3.4.21.5 0.718
2zhe 13UProthrombin 3.4.21.5 0.716
3hat GLY_VAL_ARG_RNGProthrombin 3.4.21.5 0.711
1ta2 176Prothrombin 3.4.21.5 0.710
1uvs I11Prothrombin 3.4.21.5 0.709
2zf0 51UProthrombin 3.4.21.5 0.707
4ax9 N5NProthrombin 3.4.21.5 0.705
1oyt FSNProthrombin 3.4.21.5 0.703
2zff 53UProthrombin 3.4.21.5 0.703
3qto 10PProthrombin 3.4.21.5 0.701
1wv7 5PICoagulation factor VII 3.4.21.21 0.700
1nm6 L86Prothrombin 3.4.21.5 0.699
4az2 9MUProthrombin 3.4.21.5 0.697
1mu8 CDBProthrombin 3.4.21.5 0.694
1sl3 170Prothrombin 3.4.21.5 0.694
2zp0 PI0Coagulation factor VII 3.4.21.21 0.693
2bok 784Coagulation factor X 3.4.21.6 0.692
1t4v 14AProthrombin 3.4.21.5 0.691
1mue CDDProthrombin 3.4.21.5 0.690
3dhk 23UProthrombin 3.4.21.5 0.689
3qtv 06PProthrombin 3.4.21.5 0.689
1f92 UKPUrokinase-type plasminogen activator 3.4.21.73 0.688
1gj4 132Prothrombin 3.4.21.5 0.687
1d4p BPPProthrombin 3.4.21.5 0.682
1kts C24Prothrombin 3.4.21.5 0.681
1lqd CMICoagulation factor X 3.4.21.6 0.681
1ypg UIRProthrombin 3.4.21.5 0.681
1vja 7INUrokinase-type plasminogen activator 3.4.21.73 0.680
1zrb 062Prothrombin 3.4.21.5 0.680
1xm1 GAHProthrombin 3.4.21.5 0.679
2c4f GILCoagulation factor VII 3.4.21.21 0.677
2zdv 37UProthrombin 3.4.21.5 0.676
1sb1 165Prothrombin 3.4.21.5 0.674
1z71 L17Prothrombin 3.4.21.5 0.673
3dux 64UProthrombin 3.4.21.5 0.673
4d8n 0HMKallikrein-6 3.4.21 0.671
2r2m I50Prothrombin 3.4.21.5 0.669
1c1u BAIProthrombin 3.4.21.5 0.668
2zfp 19UProthrombin 3.4.21.5 0.665
2zc9 22UProthrombin 3.4.21.5 0.664
1afe ALZProthrombin 3.4.21.5 0.663
1mu6 CDAProthrombin 3.4.21.5 0.659
3f68 91UProthrombin 3.4.21.5 0.658
1c1w BAHProthrombin 3.4.21.5 0.656
3qdz PRO_ALA_PRO_ARGProthrombin 3.4.21.5 0.654
1zsk 421Coagulation factor XI 3.4.21.27 0.651
3ens ENSCoagulation factor X 3.4.21.6 0.651
1ny2 ARG_PRO_PRO_GLYProthrombin 3.4.21.5 0.650