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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
4hdp G52 Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4hdp G52Gag-Pol polyprotein 3.4.23.16 1.353
4hdf G52Gag-Pol polyprotein 3.4.23.16 1.200
4kb9 G79Protease / 1.167
3o9c K20Pol polyprotein / 1.143
2qci 065Gag-Pol polyprotein 3.4.23.16 1.133
4hdb G52Gag-Pol polyprotein 3.4.23.16 1.133
4dfg 0JVGag-Pol polyprotein 3.4.23.16 1.117
3pwm 017Gag-Pol polyprotein 3.4.23.16 1.115
3i6o GR6Gag-Pol polyprotein 3.4.23.16 1.105
3o9h K2EGag-Pol polyprotein / 1.103
4dqc 017Gag-Pol polyprotein / 1.102
2qd6 065Gag-Pol polyprotein 3.4.23.16 1.100
3ok9 G52Gag-Pol polyprotein 3.4.23.16 1.097
3sa9 A68Protease / 1.093
2qd8 065Gag-Pol polyprotein 3.4.23.16 1.092
3oy4 017Gag-Pol polyprotein 3.4.23.16 1.088
3ecg 065Gag-Pol polyprotein 3.4.23.47 1.087
3o9a K14Pol polyprotein / 1.082
2f8g 017Gag-Pol polyprotein 3.4.23.16 1.081
4ye3 G04Gag-Pol polyprotein 3.4.23.16 1.081
3o9f K2DGag-Pol polyprotein / 1.077
4dqb 017Gag-Pol polyprotein / 1.077
2fdd 385Pol protein / 1.074
2z4o 065Gag-Pol polyprotein 3.4.23.16 1.073
3st5 G89Gag-Pol polyprotein 3.4.23.16 1.072
4q1w 017Gag-Pol polyprotein 3.4.23.16 1.072
3d1z 017Gag-Pol polyprotein 3.4.23.16 1.068
2i4d QFIProtease / 1.066
2i0a MUIProtease / 1.061
3lzv 017Gag-Pol polyprotein 3.4.23.16 1.057
1t7i 017Gag-Pol polyprotein 3.4.23.16 1.052
2f80 017Gag-Pol polyprotein 3.4.23.16 1.052
4heg G52Gag-Pol polyprotein 3.4.23.16 1.045
4dqe 017Gag-Pol polyprotein / 1.044
2f81 017Gag-Pol polyprotein 3.4.23.16 1.043
4djp M73Pol polyprotein / 1.042
3o9d K19Pol polyprotein / 1.040
3vf5 031Gag-Pol polyprotein 3.4.23.16 1.040
3vfa 031Gag-Pol polyprotein 3.4.23.16 1.039
4dqh 017Gag-Pol polyprotein / 1.039
3dk1 G05Gag-Pol polyprotein 3.4.23.16 1.038
3nuo 478Gag-Pol polyprotein 3.4.23.16 1.037
3o99 K13Pol polyprotein / 1.035
3r4b 74TGag-Pol polyprotein / 1.031
3o9b K2APol polyprotein / 1.030
3sab F78Protease / 1.030
3djk G55Gag-Pol polyprotein 3.4.23.16 1.029
4j54 G52Gag-Pol polyprotein 3.4.23.16 1.029
3t3c 017Gag-Pol polyprotein 3.4.23.16 1.027
3o9g F53Gag-Pol polyprotein / 1.026
2hb3 GRLProtease / 1.025
2qd7 065Gag-Pol polyprotein 3.4.23.16 1.025
4djo MK5Pol polyprotein / 1.022
3qaa G04Gag-Pol polyprotein 3.4.23.16 1.021
4dqf 017Gag-Pol polyprotein / 1.019
3o9e A60Pol polyprotein / 1.017
4njs G08Protease / 1.017
1t3r 017Gag-Pol polyprotein 3.4.23.16 1.015
2i4v DJRV-1 protease / 1.015
3sa8 K83Protease / 1.013
2ien 017Gag-Pol polyprotein 3.4.23.16 1.012
3gi5 K62Gag-Pol polyprotein / 1.009
3vfb 031Gag-Pol polyprotein 3.4.23.16 1.005
2i4u DJRProtease / 1.004
3saa 77FProtease / 1.004
3nu3 478Gag-Pol polyprotein 3.4.23.16 1.003
3nuj 478Gag-Pol polyprotein 3.4.23.16 1.001
2i0d MUTProtease / 0.999
2i4x KGQProtease / 0.998
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.998
2qi7 MZ9Gag-Pol polyprotein / 0.996
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.992
3ucb 017Gag-Pol polyprotein / 0.990
3oxw 017Gag-Pol polyprotein 3.4.23.16 0.988
4q1y 017Gag-Pol polyprotein 3.4.23.16 0.988
3em6 017Gag-Pol polyprotein 3.4.23.16 0.987
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.984
4q1x 017Gag-Pol polyprotein 3.4.23.16 0.984
3cyw 017Gag-Pol polyprotein 3.4.23.16 0.983
3o9i A61Gag-Pol polyprotein / 0.981
2qi5 MZ7Gag-Pol polyprotein / 0.971
3s54 017Protease / 0.970
2idw 017Protease / 0.969
2ieo 017Protease / 0.968
3sa7 55AProtease / 0.967
2qi4 MZ6Gag-Pol polyprotein / 0.966
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.961
3mxd K53Gag-Pol polyprotein 3.4.23.16 0.960
2psu MUUProtease / 0.958
3lzs 017Gag-Pol polyprotein 3.4.23.16 0.957
4j55 031Gag-Pol polyprotein 3.4.23.16 0.954
3ekv 478Gag-Pol polyprotein 3.4.23.16 0.952
3sa3 23XProtease / 0.952
3ec0 GRLGag-Pol polyprotein 3.4.23.47 0.951
2bbb HH1Gag-Pol polyprotein 3.4.23.16 0.949
3em3 478Gag-Pol polyprotein 3.4.23.16 0.949
3mxe K54Gag-Pol polyprotein 3.4.23.16 0.947
2hs1 017Protease / 0.946
4rvj 478Protease / 0.942
4djq M86Pol polyprotein / 0.940
2hs2 017Protease / 0.936
4njt 017Protease / 0.934
3vf7 031Gag-Pol polyprotein 3.4.23.16 0.933
3sa4 F72Protease / 0.924
3sac AF8Protease / 0.923
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.917
3sa6 F71Protease / 0.916
3lzu 017Gag-Pol polyprotein 3.4.23.16 0.915
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.914
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.908
3s43 478Protease / 0.903
3mws 017Pol protein / 0.901
4djr 0KJPol polyprotein / 0.898
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.896
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.895
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.895
3i7e DJRGag-Pol polyprotein / 0.893
3d20 017Gag-Pol polyprotein 3.4.23.16 0.892
3jvy 017Gag-Pol polyprotein 3.4.23.16 0.891
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.890
3gi4 K60Gag-Pol polyprotein / 0.888
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.886
4hla 017Gag-Pol polyprotein 3.4.23.16 0.886
2qi6 MZ8Gag-Pol polyprotein / 0.884
2qhy MZ1Gag-Pol polyprotein / 0.880
2qi3 MZ5Gag-Pol polyprotein / 0.880
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.875
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.873
2qi0 MZ3Gag-Pol polyprotein / 0.872
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.866
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.866
3ekt 017Gag-Pol polyprotein 3.4.23.16 0.860
3sa5 A69Protease / 0.856
3gi6 D78Gag-Pol polyprotein / 0.842
2fde 385Gag-Pol polyprotein 3.4.23.16 0.839
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.835
1hpv 478Gag-Pol polyprotein / 0.832
3sm2 478Putative gag-pro-pol polyprotein / 0.829
2nmy ROCProtease / 0.822
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.814
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.807
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.805
2qhz MZ2Gag-Pol polyprotein / 0.803
2cem 2AHPol protein / 0.799
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.797
1ida 0POGag-Pol polyprotein 3.4.23.47 0.796
2p3c 3TLProtease / 0.792
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.790
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.784
3s56 ROCProtease / 0.783
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.782
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.777
3kfr 3TLGag-Pol polyprotein / 0.772
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.771
1hih C20Gag-Pol polyprotein / 0.770
1pro A88Gag-Pol polyprotein / 0.768
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.768
3ggx GGXGag-Pol polyprotein / 0.766
1yt9 OISGag-Pol polyprotein / 0.763
1izh Q50Protease / 0.761
3ufn ROCGag-Pol polyprotein / 0.760
1bwa XV6Gag-Pol polyprotein 3.4.23.16 0.757
3s85 LK0Gag-Pol polyprotein / 0.757
2f3k RO1Protease / 0.754
2psv MUVProtease / 0.754
3kf0 3TLGag-Pol polyprotein / 0.754
1npv L27Gag-Pol polyprotein 3.4.23.16 0.753
2p3d 3TLProtease / 0.753
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.751
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.750
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.747
2fle AIProtease / 0.747
1jld 0PPGag-Pol polyprotein / 0.744
1ebz BECGag-Pol polyprotein 3.4.23.16 0.743
1hvj A78Gag-Pol polyprotein / 0.740
1hvk A79Gag-Pol polyprotein / 0.740
1hvs A77Gag-Pol polyprotein / 0.740
2nnk ROCProtease / 0.740
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.737
2nnp ROCProtease / 0.737
3kfs 3TLGag-Pol polyprotein / 0.737
2cen 4AHProtease / 0.735
1ohr 1UNV-1 PROTEASE protein / 0.733
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.733
1qbr XV6Gag-Pol polyprotein 3.4.23.16 0.732
1wbk 568Pol protein / 0.732
2i4w KGQProtease / 0.732
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.731
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.727
1qbu 846Gag-Pol polyprotein 3.4.23.16 0.727
1siv PSIGag-Pol polyprotein / 0.726
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.726
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.725
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.725
1ajv NMBGag-Pol polyprotein 3.4.23.16 0.724
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.722
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.720
2pyn 1UNGag-Pol polyprotein 3.4.23.16 0.720
2q55 MU0Protease / 0.720
3nwx KVSGag-Pol polyprotein 3.4.23.16 0.720
2hc0 AB2Protease / 0.719
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.718
3jvw DMPGag-Pol polyprotein 3.4.23.16 0.718
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.716
3kfn 3TLGag-Pol polyprotein / 0.715
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.714
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.713
3qp0 NI8Gag-Pol polyprotein 3.4.23.16 0.713
4njv RITProtease / 0.713
3bxr DRRGag-Pol polyprotein 3.4.23.16 0.711
1zsr 0ZTGag-Pol polyprotein 3.4.23.16 0.709
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.708
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.706
3gga GGWGag-Pol polyprotein / 0.706
3slz 3TLPutative gag-pro-pol polyprotein / 0.706
2uxz HI1Gag-Pol polyprotein 3.4.23.16 0.705
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.704
1hvi A77Protease / 0.704
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.704
1mui AB1Protease / 0.704
2q54 MU1Protease / 0.702
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.700
1w5x BE5Gag-Pol polyprotein 3.4.23.16 0.700
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.699
1npw LGZGag-Pol polyprotein 3.4.23.16 0.699
2bpw 1INGag-Pol polyprotein 3.4.23.16 0.698
2pwc G3GGag-Pol polyprotein 3.4.23.16 0.698
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.696
1hvr XK2Gag-Pol polyprotein / 0.696
1hxw RITGag-Pol polyprotein / 0.696
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.696
1bv7 XV6Gag-Pol polyprotein 3.4.23.16 0.694
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.694
2fxd DR7Pol polyprotein / 0.694
3qn8 NI7Gag-Pol polyprotein 3.4.23.16 0.694
3wsj MK1Protease / 0.693
1wbm BLLPol protein / 0.692
3so9 017Pol protein / 0.691
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.689
1ivq 0PXGag-Pol polyprotein / 0.689
2uy0 HV1Gag-Pol polyprotein 3.4.23.16 0.689
1hsg MK1Gag-Pol polyprotein / 0.687
1w5v BE3Gag-Pol polyprotein 3.4.23.16 0.686
1zsf 0ZSGag-Pol polyprotein 3.4.23.16 0.685
3i2l 2NCProtease / 0.685
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.684
1hpx KNIGag-Pol polyprotein / 0.682
2avm 2NCGag-Pol polyprotein 3.4.23.16 0.682
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.681
1hvl A76Gag-Pol polyprotein / 0.680
3dcr KVSProtease / 0.680
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.679
1d4h BEHGag-Pol polyprotein 3.4.23.16 0.679
2r3t G4GGag-Pol polyprotein 3.4.23.16 0.678
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.677
1hiv 1ZKGag-Pol polyprotein / 0.675
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.674
4gb2 0LQGag-Pol polyprotein 2.7.7.49 0.674
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.673
1eby BEBGag-Pol polyprotein 3.4.23.16 0.672
1g35 AHFGag-Pol polyprotein 3.4.23.16 0.672
3nls 016Gag-Pol polyprotein 3.4.23.16 0.672
1rl8 RITGag-Pol polyprotein 3.4.23.16 0.671
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.671
2aoe 0Q4Gag-Pol polyprotein 3.4.23.16 0.670
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.668
3kdc JZPGag-Pol polyprotein 3.4.23.16 0.668
3hzc 2NCProtease / 0.667
2bpy 3INGag-Pol polyprotein 3.4.23.16 0.666
3bva 2NCGag-Pol polyprotein 3.4.23.16 0.666
1hsh MK1Gag-Pol polyprotein / 0.664
1k6p XN3Gag-Pol polyprotein 3.4.23.16 0.664
1mer DMQGag-Pol polyprotein 3.4.23.16 0.664
1w5y BE6Gag-Pol polyprotein 3.4.23.16 0.661
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.660
1d4j MSCGag-Pol polyprotein 3.4.23.16 0.659
2p3a 3TLPol protein / 0.659
2qnn QN1Gag-Pol polyprotein 3.4.23.16 0.659
2qnp QN2Gag-Pol polyprotein 3.4.23.16 0.658
3kdb 006Gag-Pol polyprotein 3.4.23.16 0.658
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.657
1hos PHPGag-Pol polyprotein / 0.656
2bpz 3INGag-Pol polyprotein 3.4.23.16 0.656
1hii C20Gag-Pol polyprotein / 0.655
2b60 RITPol polyprotein / 0.655
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.654
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.654
1od1 0QSEndothiapepsin 3.4.23.22 0.653
2bqv A1AProtease / 0.653
2pk6 O33V-1 protease / 0.653
2r43 G3GGag-Pol polyprotein 3.4.23.16 0.653
2xyf G40Gag-Pol polyprotein / 0.652
3ekp 478Gag-Pol polyprotein 3.4.23.16 0.652
3nxe 2NCProtease / 0.651
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.650
2pwr G4GGag-Pol polyprotein 3.4.23.16 0.650