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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
1ypm RA4 Prothrombin 3.4.21.5

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1ypm RA4Prothrombin 3.4.21.5 1.184
2ziq 26UProthrombin 3.4.21.5 0.916
2znk 31UProthrombin 3.4.21.5 0.898
1ypl RA8Prothrombin 3.4.21.5 0.877
2zg0 50UProthrombin 3.4.21.5 0.869
4bak M67Prothrombin 3.4.21.5 0.869
4bao MVFProthrombin 3.4.21.5 0.867
2zi2 24UProthrombin 3.4.21.5 0.857
2zfq 45UProthrombin 3.4.21.5 0.851
2zhq 27UProthrombin 3.4.21.5 0.847
4ban M6SProthrombin 3.4.21.5 0.838
4baq M4ZProthrombin 3.4.21.5 0.834
2zfr 46UProthrombin 3.4.21.5 0.831
3biu 10UProthrombin 3.4.21.5 0.830
1k22 MELProthrombin 3.4.21.5 0.827
4bam MM9Prothrombin 3.4.21.5 0.825
2zhf 49UProthrombin 3.4.21.5 0.816
4bah MELProthrombin 3.4.21.5 0.813
2zgx 29UProthrombin 3.4.21.5 0.811
2zhe 13UProthrombin 3.4.21.5 0.808
3biv 11UProthrombin 3.4.21.5 0.806
2zda 32UProthrombin 3.4.21.5 0.805
4e7r 0NWProthrombin 3.4.21.5 0.804
3utu 1TSProthrombin 3.4.21.5 0.802
1c4v IH2Prothrombin 3.4.21.5 0.785
2zhw 12UProthrombin 3.4.21.5 0.785
2gde SN3Prothrombin 3.4.21.5 0.781
1ype UIPProthrombin 3.4.21.5 0.776
1riw OSCProthrombin 3.4.21.5 0.773
2v3o I26Prothrombin 3.4.21.5 0.767
1ypj UIBProthrombin 3.4.21.5 0.762
3hat GLY_VAL_ARG_RNGProthrombin 3.4.21.5 0.760
4ax9 N5NProthrombin 3.4.21.5 0.760
2cf9 348Prothrombin 3.4.21.5 0.758
2v3h I25Prothrombin 3.4.21.5 0.757
4ayy 9MXProthrombin 3.4.21.5 0.751
2cn0 F25Prothrombin 3.4.21.5 0.747
1nzq 162Prothrombin 3.4.21.5 0.744
4e5i 0N9Polymerase acidic protein / 0.744
1ypg UIRProthrombin 3.4.21.5 0.738
2cf8 ESHProthrombin 3.4.21.5 0.735
1k21 IGNProthrombin 3.4.21.5 0.733
1lpk CBBCoagulation factor X 3.4.21.6 0.725
1c5n ESIProthrombin 3.4.21.5 0.724
1t4v 14AProthrombin 3.4.21.5 0.724
4az2 9MUProthrombin 3.4.21.5 0.722
1oyt FSNProthrombin 3.4.21.5 0.721
1vzq SHYProthrombin 3.4.21.5 0.720
3dux 64UProthrombin 3.4.21.5 0.718
5cmx 0G6Prothrombin 3.4.21.5 0.715
1c4u IH1Prothrombin 3.4.21.5 0.711
2anm CDOProthrombin 3.4.21.5 0.711
1ta6 177Prothrombin 3.4.21.5 0.709
1ae8 AZLProthrombin 3.4.21.5 0.698
3qwc 98PProthrombin 3.4.21.5 0.698
3plp BBACationic trypsin 3.4.21.4 0.697
1d4p BPPProthrombin 3.4.21.5 0.696
2zf0 51UProthrombin 3.4.21.5 0.694
1ghv 120Prothrombin 3.4.21.5 0.690
1afe ALZProthrombin 3.4.21.5 0.689
2zgb 21UProthrombin 3.4.21.5 0.686
2zff 53UProthrombin 3.4.21.5 0.685
7kme ACE_0BN_CHG_PRRProthrombin 3.4.21.5 0.685
1kts C24Prothrombin 3.4.21.5 0.684
1wqv PSMCoagulation factor VII 3.4.21.21 0.681
2zdv 37UProthrombin 3.4.21.5 0.681
2a2x NA9Prothrombin 3.4.21.5 0.678
1vja 7INUrokinase-type plasminogen activator 3.4.21.73 0.676
1nt1 T76Prothrombin 3.4.21.5 0.674
3dhk 23UProthrombin 3.4.21.5 0.674
1c1u BAIProthrombin 3.4.21.5 0.671
1mue CDDProthrombin 3.4.21.5 0.670
1ta2 176Prothrombin 3.4.21.5 0.668
1ny2 ARG_PRO_PRO_GLYProthrombin 3.4.21.5 0.667
1xm1 GAHProthrombin 3.4.21.5 0.663
1zgi 382Prothrombin 3.4.21.5 0.658
1g7u PEP2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.656
2zc9 22UProthrombin 3.4.21.5 0.656
2bok 784Coagulation factor X 3.4.21.6 0.651
2pks G44Prothrombin 3.4.21.5 0.651
2zp0 PI0Coagulation factor VII 3.4.21.21 0.651
1o0d 163Prothrombin 3.4.21.5 0.650
2uuj 896Prothrombin 3.4.21.5 0.650