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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1rt4UC1Gag-Pol polyprotein2.7.7.49

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1rt4UC1Gag-Pol polyprotein2.7.7.491.000
1c1bGCAGag-Pol polyprotein2.7.7.490.661
1tl1H18Gag-Pol polyprotein2.7.7.490.629
1tl3H20Gag-Pol polyprotein2.7.7.490.604
1tkzH16Gag-Pol polyprotein2.7.7.490.601
1tktH12Gag-Pol polyprotein2.7.7.490.600
1rt2TNKGag-Pol polyprotein2.7.7.490.591
1vruAAPGag-Pol polyprotein2.7.7.490.588
4g1qT27Gag-Pol polyprotein2.7.7.490.588
2zd1T27Gag-Pol polyprotein2.7.7.490.584
3is9AC7Gag-Pol polyprotein2.7.7.490.580
3ffi3OBGag-Pol polyprotein2.7.7.490.578
4i2pG73Gag-Pol polyprotein2.7.7.490.578
1revTB9Gag-Pol polyprotein2.7.7.490.567
4id5T27Gag-Pol polyprotein2.7.7.490.566
3qlhT27Gag-Pol polyprotein2.7.7.490.561
4ifvT27Gag-Pol polyprotein2.7.7.490.558
1rt7UC4Gag-Pol polyprotein2.7.7.490.557
1s1wUC1Gag-Pol polyprotein2.7.7.490.556
1ikwEFZGag-Pol polyprotein2.7.7.490.552
1rt5UC2Gag-Pol polyprotein2.7.7.490.548
3i0rRT3Gag-Pol polyprotein2.7.7.490.539
3megT27Gag-Pol polyprotein2.7.7.490.537
2vg7NNIGag-Pol polyprotein2.7.7.490.535
2ze2T27Gag-Pol polyprotein2.7.7.490.534
4kko1REGag-Pol polyprotein2.7.7.490.533
1ikyMSDGag-Pol polyprotein2.7.7.490.532
4ig3T27Gag-Pol polyprotein2.7.7.490.532
2opqHBQGag-Pol polyprotein2.7.7.490.531
4ko0JLJGag-Pol polyprotein2.7.7.490.531
1hnvTBOGag-Pol polyprotein2.7.7.490.527
2opsHBQGag-Pol polyprotein2.7.7.490.527
1klmSPPGag-Pol polyprotein2.7.7.490.526
3dmjGWEPol protein/0.524
1jlcFTCGag-Pol polyprotein2.7.7.490.522
1jlqSBNGag-Pol polyprotein2.7.7.490.520
1hpzAAPGag-Pol polyprotein2.7.7.490.519
3m8qDJZGag-Pol polyprotein2.7.7.490.519
1jlgUC1Gag-Pol polyprotein2.7.7.490.518
2hnzPC0Gag-Pol polyprotein2.7.7.490.516
4kfbT27Gag-Pol polyprotein2.7.7.490.516
1ikxPNUGag-Pol polyprotein2.7.7.490.513
1tvrTB9Gag-Pol polyprotein2.7.7.490.513
2ban357Gag-Pol polyprotein2.7.7.490.512
1eetBFUGag-Pol polyprotein2.7.7.490.509
3lalKRVGag-Pol polyprotein2.7.7.490.509
1ikvEFZGag-Pol polyprotein2.7.7.490.508
2rf2MRXGag-Pol polyprotein2.7.7.490.508
1s6qTPBGag-Pol polyprotein2.7.7.490.507
3meeT27Gag-Pol polyprotein2.7.7.490.507
2vg5NNCGag-Pol polyprotein2.7.7.490.506
1c1c612Gag-Pol polyprotein2.7.7.490.502
1hniAAAGag-Pol polyprotein2.7.7.490.502
3i0sRT7Gag-Pol polyprotein2.7.7.490.502
4rw6494Gag-Pol polyprotein2.7.7.490.502
3mec65BGag-Pol polyprotein2.7.7.490.501
3nbpJGZGag-Pol polyprotein2.7.7.490.501
4i2q1BTGag-Pol polyprotein2.7.7.490.499
3med65BGag-Pol polyprotein2.7.7.490.496
1s9eADBGag-Pol polyprotein2.7.7.490.494
2wonZZEGag-Pol polyprotein2.7.7.490.494
2hndNVPGag-Pol polyprotein2.7.7.490.493
3irxUDRGag-Pol polyprotein2.7.7.490.492
1rt1MKCGag-Pol polyprotein2.7.7.490.490
1s1tUC1Gag-Pol polyprotein2.7.7.490.489
3m8p65BGag-Pol polyprotein2.7.7.490.489
1hquHBYGag-Pol polyprotein2.7.7.490.484
1tkxGWBGag-Pol polyprotein2.7.7.490.483
3dleGFAGag-Pol polyprotein2.7.7.490.482
1fk9EFZGag-Pol polyprotein2.7.7.490.480
2oprHBQGag-Pol polyprotein2.7.7.490.478
3t1a5MAGag-Pol polyprotein2.7.7.490.473
4j03FVSBifunctional epoxide hydrolase 23.1.3.760.469
3lanKBTGag-Pol polyprotein2.7.7.490.466
2bilBI1Serine/threonine-protein kinase pim-12.7.11.10.465
3bgrT27Gag-Pol polyprotein2.7.7.490.463
3sgx0FWDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.463
4mfb29TGag-Pol polyprotein2.7.7.490.463
4othDRNSerine/threonine-protein kinase N1/0.462
3c6uM22Gag-Pol polyprotein2.7.7.490.461
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.461
2wufKEM4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.460
4em9TCEPeroxisome proliferator-activated receptor gamma/0.459
4lmuQUESerine/threonine-protein kinase pim-12.7.11.10.458
2z3uCRRCytochrome P450/0.456
2g2hP16Tyrosine-protein kinase ABL12.7.10.20.455
3zsh469Mitogen-activated protein kinase 14/0.455
3nx4NAPPutative oxidoreductase/0.454
2b5j3ACGag-Pol polyprotein2.7.7.490.453
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.453
4a7cE46Serine/threonine-protein kinase pim-12.7.11.10.452
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.452
2oppHBQGag-Pol polyprotein2.7.7.490.450
2ph5NADHomospermidine synthase/0.449
4h4m494Gag-Pol polyprotein2.7.7.490.449
5iua6DXAdenosine receptor A2a/0.449
2ydoADNAdenosine receptor A2a/0.448
5k2dZMAAdenosine receptor A2a/0.448
4bewCZASarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.446
4lsl1YQGag-Pol polyprotein2.7.7.490.446
3th8TH9Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.445
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.445
1t1rIMB1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.444
2be2R22Gag-Pol polyprotein2.7.7.490.444
3dlgGWEGag-Pol polyprotein2.7.7.490.443
3vewADPnebramycin 5' synthase6.1.2.20.443
2hw2RFPRifampin ADP-ribosyl transferase/0.441
3dokGWJPol protein/0.441