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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
3d1z 017 Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3d1z 017Gag-Pol polyprotein 3.4.23.16 1.240
1t3r 017Gag-Pol polyprotein 3.4.23.16 1.132
3ok9 G52Gag-Pol polyprotein 3.4.23.16 1.094
3lzv 017Gag-Pol polyprotein 3.4.23.16 1.087
4q1w 017Gag-Pol polyprotein 3.4.23.16 1.082
4dqc 017Gag-Pol polyprotein / 1.080
4heg G52Gag-Pol polyprotein 3.4.23.16 1.075
3oy4 017Gag-Pol polyprotein 3.4.23.16 1.073
3nu6 478Gag-Pol polyprotein 3.4.23.16 1.072
3pwm 017Gag-Pol polyprotein 3.4.23.16 1.068
4hdp G52Gag-Pol polyprotein 3.4.23.16 1.068
4dqb 017Gag-Pol polyprotein / 1.065
3d20 017Gag-Pol polyprotein 3.4.23.16 1.062
3oxw 017Gag-Pol polyprotein 3.4.23.16 1.062
2f80 017Gag-Pol polyprotein 3.4.23.16 1.060
4dqe 017Gag-Pol polyprotein / 1.056
3o9b K2APol polyprotein / 1.055
2hs1 017Protease / 1.054
3cyw 017Gag-Pol polyprotein 3.4.23.16 1.048
2qci 065Gag-Pol polyprotein 3.4.23.16 1.045
2z4o 065Gag-Pol polyprotein 3.4.23.16 1.042
4dqf 017Gag-Pol polyprotein / 1.041
2f81 017Gag-Pol polyprotein 3.4.23.16 1.036
2qd6 065Gag-Pol polyprotein 3.4.23.16 1.035
3bvb 017Gag-Pol polyprotein 3.4.23.16 1.035
4njt 017Protease / 1.033
1t7i 017Gag-Pol polyprotein 3.4.23.16 1.031
3lzs 017Gag-Pol polyprotein 3.4.23.16 1.029
3o99 K13Pol polyprotein / 1.025
3o9e A60Pol polyprotein / 1.024
3nuj 478Gag-Pol polyprotein 3.4.23.16 1.019
2qd7 065Gag-Pol polyprotein 3.4.23.16 1.016
3t3c 017Gag-Pol polyprotein 3.4.23.16 1.007
4q1y 017Gag-Pol polyprotein 3.4.23.16 1.006
2hb3 GRLProtease / 1.005
3o9a K14Pol polyprotein / 1.005
4hdb G52Gag-Pol polyprotein 3.4.23.16 1.004
3o9c K20Pol polyprotein / 1.001
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.999
3em6 017Gag-Pol polyprotein 3.4.23.16 0.996
4dqh 017Gag-Pol polyprotein / 0.991
2i4u DJRProtease / 0.989
4hdf G52Gag-Pol polyprotein 3.4.23.16 0.980
2f8g 017Gag-Pol polyprotein 3.4.23.16 0.976
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.976
3qaa G04Gag-Pol polyprotein 3.4.23.16 0.976
3s54 017Protease / 0.975
3ucb 017Gag-Pol polyprotein / 0.972
2qd8 065Gag-Pol polyprotein 3.4.23.16 0.970
3o9i A61Gag-Pol polyprotein / 0.970
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.970
4rvj 478Protease / 0.966
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.965
2fdd 385Pol protein / 0.962
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.962
3mws 017Pol protein / 0.962
3o9f K2DGag-Pol polyprotein / 0.962
2ien 017Gag-Pol polyprotein 3.4.23.16 0.961
3st5 G89Gag-Pol polyprotein 3.4.23.16 0.961
3lzu 017Gag-Pol polyprotein 3.4.23.16 0.960
4kb9 G79Protease / 0.960
3ecg 065Gag-Pol polyprotein 3.4.23.47 0.958
2idw 017Protease / 0.956
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.955
2i4d QFIProtease / 0.954
3djk G55Gag-Pol polyprotein 3.4.23.16 0.953
3o9h K2EGag-Pol polyprotein / 0.953
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.952
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.948
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.947
3dk1 G05Gag-Pol polyprotein 3.4.23.16 0.945
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.943
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.926
2qi4 MZ6Gag-Pol polyprotein / 0.924
3vf5 031Gag-Pol polyprotein 3.4.23.16 0.924
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.924
2ieo 017Protease / 0.923
3vf7 031Gag-Pol polyprotein 3.4.23.16 0.922
3sa8 K83Protease / 0.920
3i6o GR6Gag-Pol polyprotein 3.4.23.16 0.919
2qi0 MZ3Gag-Pol polyprotein / 0.916
4djp M73Pol polyprotein / 0.915
3em3 478Gag-Pol polyprotein 3.4.23.16 0.911
3i7e DJRGag-Pol polyprotein / 0.911
3sa9 A68Protease / 0.910
3vfa 031Gag-Pol polyprotein 3.4.23.16 0.907
4hla 017Gag-Pol polyprotein 3.4.23.16 0.907
3r4b 74TGag-Pol polyprotein / 0.906
2hs2 017Protease / 0.902
2i0d MUTProtease / 0.902
2i4v DJRV-1 protease / 0.901
3gi5 K62Gag-Pol polyprotein / 0.897
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.897
3gi6 D78Gag-Pol polyprotein / 0.895
3mxd K53Gag-Pol polyprotein 3.4.23.16 0.894
4njs G08Protease / 0.893
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.887
3sa6 F71Protease / 0.887
3o9g F53Gag-Pol polyprotein / 0.885
2psu MUUProtease / 0.883
3sa7 55AProtease / 0.882
2i0a MUIProtease / 0.875
2qi6 MZ8Gag-Pol polyprotein / 0.871
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.871
4j54 G52Gag-Pol polyprotein 3.4.23.16 0.871
4djq M86Pol polyprotein / 0.870
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.869
3gi4 K60Gag-Pol polyprotein / 0.867
3o9d K19Pol polyprotein / 0.863
4djo MK5Pol polyprotein / 0.861
3sa3 23XProtease / 0.858
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.858
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.856
2qi5 MZ7Gag-Pol polyprotein / 0.854
3sac AF8Protease / 0.853
3s43 478Protease / 0.851
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.849
2qhy MZ1Gag-Pol polyprotein / 0.848
4j55 031Gag-Pol polyprotein 3.4.23.16 0.845
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.842
2qi3 MZ5Gag-Pol polyprotein / 0.839
4djr 0KJPol polyprotein / 0.829
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.827
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.826
3sm2 478Putative gag-pro-pol polyprotein / 0.824
3saa 77FProtease / 0.823
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.816
3sab F78Protease / 0.816
2qi1 MZ4Gag-Pol polyprotein / 0.813
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.811
3sa4 F72Protease / 0.809
1npv L27Gag-Pol polyprotein 3.4.23.16 0.808
2i4x KGQProtease / 0.807
3sa5 A69Protease / 0.804
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.796
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.795
2qi7 MZ9Gag-Pol polyprotein / 0.795
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.787
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.778
3s85 LK0Gag-Pol polyprotein / 0.773
2p3c 3TLProtease / 0.772
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.770
1t7j 478Gag-Pol polyprotein 3.4.23.16 0.769
2qhz MZ2Gag-Pol polyprotein / 0.764
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.764
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.763
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.762
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.757
3s56 ROCProtease / 0.752
1hpv 478Gag-Pol polyprotein / 0.750
2psv MUVProtease / 0.750
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.750
2fde 385Gag-Pol polyprotein 3.4.23.16 0.746
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.746
4k4p 3TLGag-Pol polyprotein / 0.745
3ekx 1UNGag-Pol polyprotein 3.4.23.16 0.743
2p3a 3TLPol protein / 0.741
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.740
2q54 MU1Protease / 0.739
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.737
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.737
3fx5 KNIGag-Pol polyprotein 3.4.23.16 0.737
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.736
2f3k RO1Protease / 0.735
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.733
2nmy ROCProtease / 0.733
3ndt ROCGag-Pol polyprotein 3.4.23.16 0.731
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.730
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.727
2nnp ROCProtease / 0.723
2p3d 3TLProtease / 0.722
3a2o KNJGag-Pol polyprotein 3.4.23.16 0.721
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.721
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.720
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.719
1yt9 OISGag-Pol polyprotein / 0.718
2hc0 AB2Protease / 0.717
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.717
2wl0 5AHGag-Pol polyprotein / 0.716
3kfn 3TLGag-Pol polyprotein / 0.714
1xl5 190Gag-Pol polyprotein 3.4.23.16 0.713
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.712
2nnk ROCProtease / 0.712
2i4w KGQProtease / 0.711
2r3t G4GGag-Pol polyprotein 3.4.23.16 0.711
3ufn ROCGag-Pol polyprotein / 0.709
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.708
2uy0 HV1Gag-Pol polyprotein 3.4.23.16 0.708
3gga GGWGag-Pol polyprotein / 0.708
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.707
1npw LGZGag-Pol polyprotein 3.4.23.16 0.707
1ohr 1UNV-1 PROTEASE protein / 0.705
2pk6 O33V-1 protease / 0.703
2r38 G4GGag-Pol polyprotein 3.4.23.16 0.703
3kdc JZPGag-Pol polyprotein 3.4.23.16 0.703
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.702
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.702
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.702
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.701
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.699
2fle AIProtease / 0.698
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.698
1daz 0Q4Gag-Pol polyprotein 3.4.23.16 0.697
1k1u 0Q4Gag-Pol polyprotein 3.4.23.16 0.697
2cen 4AHProtease / 0.697
1sbg IM1Gag-Pol polyprotein / 0.693
2p3b 3TLV-1 PROTEASE protein / 0.693
2p3b 3TLV-1 protease / 0.693
3kf0 3TLGag-Pol polyprotein / 0.693
1izh Q50Protease / 0.692
3hzc 2NCProtease / 0.692
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.691
3slz 3TLPutative gag-pro-pol polyprotein / 0.691
3nls 016Gag-Pol polyprotein 3.4.23.16 0.690
1msm JE2Gag-Pol polyprotein 3.4.23.16 0.689
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.689
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.688
3kfr 3TLGag-Pol polyprotein / 0.688
1hxb ROCGag-Pol polyprotein 3.4.23.16 0.686
1ida 0POGag-Pol polyprotein 3.4.23.47 0.686
1sh9 RITGag-Pol polyprotein 3.4.23.16 0.686
9hvp 0E9Gag-Pol polyprotein / 0.686
1hih C20Gag-Pol polyprotein / 0.685
3ndx RITGag-Pol polyprotein 3.4.23.16 0.684
1g35 AHFGag-Pol polyprotein 3.4.23.16 0.681
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.681
3ndw RITGag-Pol polyprotein 3.4.23.16 0.680
1k2b 0Q4Gag-Pol polyprotein 3.4.23.16 0.679
1msn JE2Gag-Pol polyprotein 3.4.23.16 0.679
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.679
2b60 RITPol polyprotein / 0.678
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.677
1wbm BLLPol protein / 0.677
1d4j MSCGag-Pol polyprotein 3.4.23.16 0.675
3nwq 2NCGag-Pol polyprotein 3.4.23.16 0.675
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.673
2q55 MU0Protease / 0.673
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.672
3kdb 006Gag-Pol polyprotein 3.4.23.16 0.672
1siv PSIGag-Pol polyprotein / 0.671
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.669
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.669
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.669
2cem 2AHPol protein / 0.669
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.669
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.668
1hsg MK1Gag-Pol polyprotein / 0.668
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.668
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.667
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.667
1hvj A78Gag-Pol polyprotein / 0.665
1odw 0E8Gag-Pol polyprotein 3.4.23.16 0.664
1hpx KNIGag-Pol polyprotein / 0.663
1hiv 1ZKGag-Pol polyprotein / 0.662
1mer DMQGag-Pol polyprotein 3.4.23.16 0.662
2qhc AB1Protease / 0.662
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.661
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.661
1ec0 BEDGag-Pol polyprotein 3.4.23.16 0.661
1k6p XN3Gag-Pol polyprotein 3.4.23.16 0.661
3dck KVIProtease / 0.660
3i2l 2NCProtease / 0.660
1kzk JE2Gag-Pol polyprotein 3.4.23.16 0.659
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.658
3so9 017Pol protein / 0.657
1ivq 0PXGag-Pol polyprotein / 0.656
3qn8 NI7Gag-Pol polyprotein 3.4.23.16 0.656
2wkz 5AHGag-Pol polyprotein / 0.654
3el5 1UNGag-Pol polyprotein / 0.654
1dif A85Gag-Pol polyprotein / 0.652
2avv MK1Gag-Pol polyprotein 3.4.23.16 0.652
1fg8 0Q4Gag-Pol polyprotein 3.4.23.16 0.651