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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3m8p65BGag-Pol polyprotein2.7.7.49

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3m8p65BGag-Pol polyprotein2.7.7.491.000
3mec65BGag-Pol polyprotein2.7.7.490.632
3nbpJGZGag-Pol polyprotein2.7.7.490.621
3m8qDJZGag-Pol polyprotein2.7.7.490.607
3med65BGag-Pol polyprotein2.7.7.490.600
4i2q1BTGag-Pol polyprotein2.7.7.490.559
2ze2T27Gag-Pol polyprotein2.7.7.490.558
3qlhT27Gag-Pol polyprotein2.7.7.490.546
3megT27Gag-Pol polyprotein2.7.7.490.531
4i2pG73Gag-Pol polyprotein2.7.7.490.528
3meeT27Gag-Pol polyprotein2.7.7.490.526
4g1qT27Gag-Pol polyprotein2.7.7.490.523
3is9AC7Gag-Pol polyprotein2.7.7.490.521
1eetBFUGag-Pol polyprotein2.7.7.490.519
1s9eADBGag-Pol polyprotein2.7.7.490.515
2hnzPC0Gag-Pol polyprotein2.7.7.490.513
4id5T27Gag-Pol polyprotein2.7.7.490.509
4rw6494Gag-Pol polyprotein2.7.7.490.509
1ikyMSDGag-Pol polyprotein2.7.7.490.507
3i0sRT7Gag-Pol polyprotein2.7.7.490.507
1tl3H20Gag-Pol polyprotein2.7.7.490.506
1s6qTPBGag-Pol polyprotein2.7.7.490.505
2zd1T27Gag-Pol polyprotein2.7.7.490.501
3lanKBTGag-Pol polyprotein2.7.7.490.500
1c1bGCAGag-Pol polyprotein2.7.7.490.498
3bgrT27Gag-Pol polyprotein2.7.7.490.498
1ikwEFZGag-Pol polyprotein2.7.7.490.497
1fk9EFZGag-Pol polyprotein2.7.7.490.493
1tl1H18Gag-Pol polyprotein2.7.7.490.492
3i0rRT3Gag-Pol polyprotein2.7.7.490.492
1tvrTB9Gag-Pol polyprotein2.7.7.490.490
1hpzAAPGag-Pol polyprotein2.7.7.490.487
1rt4UC1Gag-Pol polyprotein2.7.7.490.486
3irxUDRGag-Pol polyprotein2.7.7.490.486
2rf2MRXGag-Pol polyprotein2.7.7.490.485
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.484
2vg7NNIGag-Pol polyprotein2.7.7.490.484
1jlcFTCGag-Pol polyprotein2.7.7.490.483
4ifvT27Gag-Pol polyprotein2.7.7.490.482
1revTB9Gag-Pol polyprotein2.7.7.490.481
4kko1REGag-Pol polyprotein2.7.7.490.480
4o0rX4ZSerine/threonine-protein kinase PAK 12.7.11.10.480
1rt5UC2Gag-Pol polyprotein2.7.7.490.479
3lamKRPGag-Pol polyprotein2.7.7.490.479
3sgtP09Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)/0.478
1tktH12Gag-Pol polyprotein2.7.7.490.477
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.475
1osvCHCBile acid receptor/0.475
1rt7UC4Gag-Pol polyprotein2.7.7.490.474
1ikvEFZGag-Pol polyprotein2.7.7.490.473
4ele31IDihydrofolate reductase/0.473
4ko0JLJGag-Pol polyprotein2.7.7.490.473
3ffi3OBGag-Pol polyprotein2.7.7.490.472
3frqERYErythromycin resistance repressor protein/0.471
4ig3T27Gag-Pol polyprotein2.7.7.490.470
3lj3WYEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.469
1s1wUC1Gag-Pol polyprotein2.7.7.490.467
4i7fNVEGag-Pol polyprotein2.7.7.490.467
3h0aD30Peroxisome proliferator-activated receptor gamma/0.465
5cyqT27Gag-Pol polyprotein2.7.7.490.465
1hniAAAGag-Pol polyprotein2.7.7.490.464
3fl8RARDihydrofolate reductase/0.463
3lalKRVGag-Pol polyprotein2.7.7.490.463
3vt5YI2Vitamin D3 receptor/0.463
1hnvTBOGag-Pol polyprotein2.7.7.490.462
3l8p0CEAngiopoietin-1 receptor2.7.10.10.461
4c4h7RODual specificity protein kinase TTK2.7.12.10.461
4fhh0U3Vitamin D3 receptor A/0.461
4kfbT27Gag-Pol polyprotein2.7.7.490.461
3w0aDS5Vitamin D3 receptor/0.460
4bidIE8Mitogen-activated protein kinase kinase kinase 52.7.11.250.460
4c4f7CEDual specificity protein kinase TTK2.7.12.10.460
3vt8YI3Vitamin D3 receptor/0.459
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.459
2y46MIVMycinamicin IV hydroxylase/epoxidase/0.458
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
2p4yC03Peroxisome proliferator-activated receptor gamma/0.457
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.457
2wufKEM4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.456
4jbqVX6Aurora kinase A2.7.11.10.456
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.456
1rt2TNKGag-Pol polyprotein2.7.7.490.455
3nalDBKCalcium-transporting ATPase/0.455
1hquHBYGag-Pol polyprotein2.7.7.490.454
1ie4T44Transthyretin/0.454
2hb7O1CVitamin D3 receptor/0.454
2q5g1FAPeroxisome proliferator-activated receptor delta/0.454
1jlgUC1Gag-Pol polyprotein2.7.7.490.453
3nc9TR3Ketohexokinase/0.453
3reyXACAdenosine receptor A2a/0.453
3icrCOACoenzyme A disulfide reductase/0.452
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.452
1s0zEB1Vitamin D3 receptor/0.451
3vs2VSBTyrosine-protein kinase HCK2.7.10.20.451
3vt3VDXVitamin D3 receptor/0.451
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.451
4mcv29KProto-oncogene tyrosine-protein kinase Src2.7.10.20.451
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1vruAAPGag-Pol polyprotein2.7.7.490.450
3s2a2NQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
3vt45YIVitamin D3 receptor/0.450
4mfb29TGag-Pol polyprotein2.7.7.490.450
1ot7CHCBile acid receptor/0.449
3dmjGWEPol protein/0.449
3kpzZNEVitamin D3 receptor/0.449
3w0jT08Vitamin D3 receptor/0.449
3w1f1O5Dual specificity protein kinase TTK2.7.12.10.449
4lsl1YQGag-Pol polyprotein2.7.7.490.449
1txiTX5Vitamin D3 receptor/0.448
3h1jSMACytochrome b/0.448
3vs5VSGTyrosine-protein kinase HCK2.7.10.20.448
1hvyD16Thymidylate synthase2.1.1.450.446
1klmSPPGag-Pol polyprotein2.7.7.490.446
2hy81STSerine/threonine-protein kinase PAK 12.7.11.10.446
2y00Y01Beta-1 adrenergic receptor/0.446
3gubGUBDeath-associated protein kinase 12.7.11.10.446
3zk5Z18Cytochrome P450 monooxygenase PikC/0.446
4kz01UJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
1jlqSBNGag-Pol polyprotein2.7.7.490.445
1zeoC01Peroxisome proliferator-activated receptor gamma/0.445
2b5j3ACGag-Pol polyprotein2.7.7.490.445
3vt65YIVitamin D3 receptor/0.445
4fkv61KCyclin-dependent kinase 22.7.11.220.445
4g1y0VOVitamin D3 receptor A/0.445
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.445
4o71CPBBromodomain-containing protein 4/0.445
2ban357Gag-Pol polyprotein2.7.7.490.444
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.444
2opsHBQGag-Pol polyprotein2.7.7.490.444
3dokGWJPol protein/0.444
4fhi0S4Vitamin D3 receptor A/0.444
4h4m494Gag-Pol polyprotein2.7.7.490.444
1yinCM3Estrogen receptor/0.443
2w3vTOPDihydrofolate reductase/0.443
3p7nFMNLight-activated DNA-binding protein EL222/0.443
4dk50KOPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1s19MC9Vitamin D3 receptor/0.442
1uzwCDHIsopenicillin N synthase1.21.3.10.442
1yb5NAPQuinone oxidoreductase1.6.5.50.442
2cdz23DSerine/threonine-protein kinase PAK 42.7.11.10.442
2y02Y01Beta-1 adrenergic receptor/0.442
2zjwREFCasein kinase II subunit alpha2.7.11.10.442
3a4oSTUTyrosine-protein kinase Lyn2.7.10.20.442
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
3th8TH9Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.442
3vrzVRZTyrosine-protein kinase HCK2.7.10.20.442
4nieNBHNuclear receptor ROR-gamma/0.442
2aibERGBeta-elicitin cinnamomin/0.441
2hcdBIVVitamin D3 receptor A/0.441
2q61SF1Peroxisome proliferator-activated receptor gamma/0.441
3slkNDPPolyketide synthase extender module 2/0.441
3vt9YI4Vitamin D3 receptor/0.441
3wixLC3Induced myeloid leukemia cell differentiation protein Mcl-1/0.441
4elf35IDihydrofolate reductase/0.441
4gk4L90Ephrin type-A receptor 32.7.10.10.441
4y8wSTRSteroid 21-hydroxylase/0.441
1ezvSMACytochrome b/0.440
2j0m4STFocal adhesion kinase 12.7.10.20.440
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.440
4neuQ1AReceptor-interacting serine/threonine-protein kinase 12.7.11.10.440