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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
3oy4 017 Gag-Pol polyprotein 3.4.23.16

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3oy4 017Gag-Pol polyprotein 3.4.23.16 1.345
3o9b K2APol polyprotein / 1.296
4q1w 017Gag-Pol polyprotein 3.4.23.16 1.296
3o9a K14Pol polyprotein / 1.295
1t3r 017Gag-Pol polyprotein 3.4.23.16 1.275
3o9g F53Gag-Pol polyprotein / 1.256
3o9f K2DGag-Pol polyprotein / 1.253
3o9c K20Pol polyprotein / 1.244
4dqf 017Gag-Pol polyprotein / 1.244
3o9e A60Pol polyprotein / 1.240
3o9d K19Pol polyprotein / 1.237
3lzv 017Gag-Pol polyprotein 3.4.23.16 1.235
4dqc 017Gag-Pol polyprotein / 1.235
4dqb 017Gag-Pol polyprotein / 1.234
3o9h K2EGag-Pol polyprotein / 1.231
4dqh 017Gag-Pol polyprotein / 1.224
4dqe 017Gag-Pol polyprotein / 1.222
3o99 K13Pol polyprotein / 1.216
3pwm 017Gag-Pol polyprotein 3.4.23.16 1.212
2hb3 GRLProtease / 1.192
2qd7 065Gag-Pol polyprotein 3.4.23.16 1.187
2idw 017Protease / 1.183
3o9i A61Gag-Pol polyprotein / 1.168
2f80 017Gag-Pol polyprotein 3.4.23.16 1.164
1t7i 017Gag-Pol polyprotein 3.4.23.16 1.162
3em6 017Gag-Pol polyprotein 3.4.23.16 1.156
3sa8 K83Protease / 1.153
3ecg 065Gag-Pol polyprotein 3.4.23.47 1.148
3t3c 017Gag-Pol polyprotein 3.4.23.16 1.140
4heg G52Gag-Pol polyprotein 3.4.23.16 1.138
2qci 065Gag-Pol polyprotein 3.4.23.16 1.129
4njs G08Protease / 1.129
3r4b 74TGag-Pol polyprotein / 1.122
2i4u DJRProtease / 1.115
3oxw 017Gag-Pol polyprotein 3.4.23.16 1.113
3st5 G89Gag-Pol polyprotein 3.4.23.16 1.112
2hs1 017Protease / 1.111
4q1y 017Gag-Pol polyprotein 3.4.23.16 1.111
3ekv 478Gag-Pol polyprotein 3.4.23.16 1.108
4q1x 017Gag-Pol polyprotein 3.4.23.16 1.108
3d20 017Gag-Pol polyprotein 3.4.23.16 1.107
2i0a MUIProtease / 1.103
3dk1 G05Gag-Pol polyprotein 3.4.23.16 1.100
3ok9 G52Gag-Pol polyprotein 3.4.23.16 1.097
2f81 017Gag-Pol polyprotein 3.4.23.16 1.096
3vf7 031Gag-Pol polyprotein 3.4.23.16 1.094
4hdp G52Gag-Pol polyprotein 3.4.23.16 1.088
3vfa 031Gag-Pol polyprotein 3.4.23.16 1.080
2i4d QFIProtease / 1.079
4njt 017Protease / 1.077
3d1z 017Gag-Pol polyprotein 3.4.23.16 1.073
3gi4 K60Gag-Pol polyprotein / 1.072
3djk G55Gag-Pol polyprotein 3.4.23.16 1.069
2ien 017Gag-Pol polyprotein 3.4.23.16 1.065
4djo MK5Pol polyprotein / 1.061
3ucb 017Gag-Pol polyprotein / 1.060
2qi6 MZ8Gag-Pol polyprotein / 1.059
3vf5 031Gag-Pol polyprotein 3.4.23.16 1.058
2psu MUUProtease / 1.057
3jvy 017Gag-Pol polyprotein 3.4.23.16 1.057
2qi4 MZ6Gag-Pol polyprotein / 1.055
3mws 017Pol protein / 1.054
2i4v DJRV-1 protease / 1.051
4djp M73Pol polyprotein / 1.049
3mxd K53Gag-Pol polyprotein 3.4.23.16 1.045
3lzu 017Gag-Pol polyprotein 3.4.23.16 1.043
3ec0 GRLGag-Pol polyprotein 3.4.23.47 1.042
2qd8 065Gag-Pol polyprotein 3.4.23.16 1.041
3qaa G04Gag-Pol polyprotein 3.4.23.16 1.041
3sa9 A68Protease / 1.040
3i7e DJRGag-Pol polyprotein / 1.036
3sa4 F72Protease / 1.029
2qd6 065Gag-Pol polyprotein 3.4.23.16 1.028
2z4o 065Gag-Pol polyprotein 3.4.23.16 1.028
3ekt 017Gag-Pol polyprotein 3.4.23.16 1.027
2f8g 017Gag-Pol polyprotein 3.4.23.16 1.024
2ieo 017Protease / 1.021
4kb9 G79Protease / 1.021
4hdf G52Gag-Pol polyprotein 3.4.23.16 1.020
3i6o GR6Gag-Pol polyprotein 3.4.23.16 1.014
3lzs 017Gag-Pol polyprotein 3.4.23.16 1.014
3mxe K54Gag-Pol polyprotein 3.4.23.16 1.013
4djq M86Pol polyprotein / 1.012
3s54 017Protease / 1.007
2qi7 MZ9Gag-Pol polyprotein / 1.004
4j54 G52Gag-Pol polyprotein 3.4.23.16 1.004
3gi5 K62Gag-Pol polyprotein / 1.003
3gi6 D78Gag-Pol polyprotein / 1.002
2fdd 385Pol protein / 0.999
2qi0 MZ3Gag-Pol polyprotein / 0.995
3em3 478Gag-Pol polyprotein 3.4.23.16 0.991
4i8z G08Gag-Pol polyprotein 3.4.23.16 0.989
3sac AF8Protease / 0.987
4djr 0KJPol polyprotein / 0.987
3sa7 55AProtease / 0.985
3cyw 017Gag-Pol polyprotein 3.4.23.16 0.981
3sab F78Protease / 0.981
2i4x KGQProtease / 0.980
3saa 77FProtease / 0.975
2qhy MZ1Gag-Pol polyprotein / 0.968
3jw2 017Gag-Pol polyprotein 3.4.23.16 0.966
4dfg 0JVGag-Pol polyprotein 3.4.23.16 0.966
2i0d MUTProtease / 0.962
3nu9 478Gag-Pol polyprotein 3.4.23.16 0.961
3nuj 478Gag-Pol polyprotein 3.4.23.16 0.961
3nu4 478Gag-Pol polyprotein 3.4.23.16 0.959
2hs2 017Protease / 0.954
3oxv 478Gag-Pol polyprotein 3.4.23.16 0.954
3nu3 478Gag-Pol polyprotein 3.4.23.16 0.952
3ggu 017Gag-Pol polyprotein 3.4.23.16 0.951
1z1r HBHGag-Pol polyprotein 3.4.23.16 0.946
2qi5 MZ7Gag-Pol polyprotein / 0.941
3sa6 F71Protease / 0.940
2fde 385Gag-Pol polyprotein 3.4.23.16 0.938
3nu5 478Gag-Pol polyprotein 3.4.23.16 0.934
4j55 031Gag-Pol polyprotein 3.4.23.16 0.934
3vfb 031Gag-Pol polyprotein 3.4.23.16 0.932
3sa3 23XProtease / 0.925
3nuo 478Gag-Pol polyprotein 3.4.23.16 0.920
4hla 017Gag-Pol polyprotein 3.4.23.16 0.917
4ye3 G04Gag-Pol polyprotein 3.4.23.16 0.916
4rvj 478Protease / 0.902
3nu6 478Gag-Pol polyprotein 3.4.23.16 0.894
4hdb G52Gag-Pol polyprotein 3.4.23.16 0.893
4j5j 478Gag-Pol polyprotein 3.4.23.16 0.892
2qhz MZ2Gag-Pol polyprotein / 0.880
2psv MUVProtease / 0.876
2qi3 MZ5Gag-Pol polyprotein / 0.869
3s43 478Protease / 0.869
3sm2 478Putative gag-pro-pol polyprotein / 0.867
1d4l PI9Gag-Pol polyprotein 3.4.23.16 0.863
1hpv 478Gag-Pol polyprotein / 0.854
1z1h HBBGag-Pol polyprotein 3.4.23.16 0.851
3sa5 A69Protease / 0.850
1npv L27Gag-Pol polyprotein 3.4.23.16 0.839
3eky DR7Gag-Pol polyprotein 3.4.23.16 0.831
3oxx DR7Gag-Pol polyprotein 3.4.23.16 0.816
1b6l PI4Gag-Pol polyprotein 3.4.23.16 0.814
3el9 DR7Gag-Pol polyprotein 3.4.23.16 0.810
2nmy ROCProtease / 0.805
3s85 LK0Gag-Pol polyprotein / 0.792
1npa 3NHGag-Pol polyprotein 3.4.23.16 0.783
1npw LGZGag-Pol polyprotein 3.4.23.16 0.783
2bb9 AKCGag-Pol polyprotein 3.4.23.16 0.775
1b6k PI5Gag-Pol polyprotein 3.4.23.16 0.772
3kfn 3TLGag-Pol polyprotein / 0.772
1ida 0POGag-Pol polyprotein 3.4.23.47 0.767
3k4v ROCGag-Pol polyprotein 3.4.23.16 0.763
4qgi ROCGag-Pol polyprotein 3.4.23.16 0.761
2qak 1UNGag-Pol polyprotein 3.4.23.16 0.758
1izh Q50Protease / 0.755
3tl9 ROCGag-Pol polyprotein 3.4.23.16 0.754
1yt9 OISGag-Pol polyprotein / 0.753
3em4 DR7Gag-Pol polyprotein 3.4.23.16 0.753
2fxe DR7Gag-Pol polyprotein 3.4.23.16 0.750
3s56 ROCProtease / 0.744
2q63 1UNGag-Pol polyprotein 3.4.23.16 0.743
3bvb 017Gag-Pol polyprotein 3.4.23.16 0.743
3slz 3TLPutative gag-pro-pol polyprotein / 0.743
1hih C20Gag-Pol polyprotein / 0.740
3el4 ROCGag-Pol polyprotein 3.4.23.16 0.740
3ufn ROCGag-Pol polyprotein / 0.739
1t7j 478Gag-Pol polyprotein 3.4.23.16 0.738
2hc0 AB2Protease / 0.738
2pym 1UNGag-Pol polyprotein 3.4.23.16 0.736
3ekq ROCGag-Pol polyprotein 3.4.23.16 0.736
3el0 1UNGag-Pol polyprotein 3.4.23.16 0.736
1izi Q50Gag-Pol polyprotein 3.4.23.16 0.734
2nnp ROCProtease / 0.732
1ohr 1UNV-1 PROTEASE protein / 0.731
1mrw K57Gag-Pol polyprotein 3.4.23.16 0.728
1ivq 0PXGag-Pol polyprotein / 0.725
2nnk ROCProtease / 0.725
3el1 DR7Gag-Pol polyprotein 3.4.23.16 0.723
3cyx ROCGag-Pol polyprotein 3.4.23.16 0.722
2cen 4AHProtease / 0.720
1ec1 BEEGag-Pol polyprotein 3.4.23.16 0.716
1tcx IM1Gag-Pol polyprotein 3.4.23.16 0.716
3ggx GGXGag-Pol polyprotein / 0.715
1k6t XN1Gag-Pol polyprotein 3.4.23.16 0.714
3d1x ROCGag-Pol polyprotein 3.4.23.16 0.713
3d1y ROCGag-Pol polyprotein 3.4.23.16 0.713
3gga GGWGag-Pol polyprotein / 0.713
1sdv MK1Gag-Pol polyprotein 3.4.23.16 0.712
1a94 0Q4Gag-Pol polyprotein 3.4.23.16 0.710
1hvk A79Gag-Pol polyprotein / 0.710
2f3k RO1Protease / 0.710
1mtr PI6Gag-Pol polyprotein 3.4.23.16 0.709
3kfr 3TLGag-Pol polyprotein / 0.707
3pwr ROCGag-Pol polyprotein 3.4.23.16 0.707
1ffi 2NCGag-Pol polyprotein 3.4.23.16 0.706
3kfs 3TLGag-Pol polyprotein / 0.706
3jvw DMPGag-Pol polyprotein 3.4.23.16 0.704
2avs MK1Gag-Pol polyprotein 3.4.23.16 0.703
1jld 0PPGag-Pol polyprotein / 0.701
1c6y MK1Protease / 0.700
2bpw 1INGag-Pol polyprotein 3.4.23.16 0.695
3ekw DR7Gag-Pol polyprotein 3.4.23.16 0.695
1meu DMPGag-Pol polyprotein 3.4.23.16 0.694
1pro A88Gag-Pol polyprotein / 0.694
1mrx K57Gag-Pol polyprotein 3.4.23.16 0.692
1qbt 146Gag-Pol polyprotein 3.4.23.16 0.690
2a1e IPFGag-Pol polyprotein 3.4.23.16 0.689
1m0b 0ZQGag-Pol polyprotein 3.4.23.16 0.686
1qbr XV6Gag-Pol polyprotein 3.4.23.16 0.686
1sdu MK1Gag-Pol polyprotein 3.4.23.16 0.686
2q64 1UNGag-Pol polyprotein 3.4.23.16 0.686
1a8g 2Z4Gag-Pol polyprotein 3.4.23.16 0.685
1bdr IM1Gag-Pol polyprotein 3.4.23.16 0.684
3ttp 017Gag-Pol polyprotein 3.4.23.16 0.684
1idb 0DOGag-Pol polyprotein / 0.683
2bqv A1AProtease / 0.683
3so9 017Pol protein / 0.682
2wkz 5AHGag-Pol polyprotein / 0.681
1ajv NMBGag-Pol polyprotein 3.4.23.16 0.680
1sdt MK1Gag-Pol polyprotein 3.4.23.16 0.680
1b6p PI7Gag-Pol polyprotein 3.4.23.16 0.679
1bv7 XV6Gag-Pol polyprotein 3.4.23.16 0.679
1fg6 2NCGag-Pol polyprotein 3.4.23.16 0.678
2aqu DR7Gag-Pol polyprotein 3.4.23.16 0.677
2q54 MU1Protease / 0.677
1fff 0Q4Gag-Pol polyprotein 3.4.23.16 0.670
1ec2 BEJGag-Pol polyprotein 3.4.23.16 0.666
1fej 2NCGag-Pol polyprotein 3.4.23.16 0.666
1a9m U0EGag-Pol polyprotein / 0.665
1ff0 2NCGag-Pol polyprotein 3.4.23.16 0.665
3dm6 757Beta-secretase 1 3.4.23.46 0.664
3nxe 2NCProtease / 0.664
1fgc 2NCGag-Pol polyprotein 3.4.23.16 0.663
1hiv 1ZKGag-Pol polyprotein / 0.662
1k2c 0Q4Gag-Pol polyprotein 3.4.23.16 0.659
2p3d 3TLProtease / 0.659
3nyg 2NCGag-Pol polyprotein 3.4.23.16 0.659
1d4i BEGGag-Pol polyprotein 3.4.23.16 0.657
1sbg IM1Gag-Pol polyprotein / 0.657
3i2l 2NCProtease / 0.657
2z54 AB1Gag-Pol polyprotein 3.4.23.16 0.656
1ec3 MS3Gag-Pol polyprotein 3.4.23.16 0.655
1hvr XK2Gag-Pol polyprotein / 0.654
1hvj A78Gag-Pol polyprotein / 0.653
1b6m PI6Gag-Pol polyprotein 3.4.23.16 0.652