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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
1ikyMSDGag-Pol polyprotein2.7.7.49

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1ikyMSDGag-Pol polyprotein2.7.7.491.000
1ikxPNUGag-Pol polyprotein2.7.7.490.602
2ze2T27Gag-Pol polyprotein2.7.7.490.582
1tl1H18Gag-Pol polyprotein2.7.7.490.581
1vruAAPGag-Pol polyprotein2.7.7.490.581
3is9AC7Gag-Pol polyprotein2.7.7.490.569
1rt4UC1Gag-Pol polyprotein2.7.7.490.560
1tl3H20Gag-Pol polyprotein2.7.7.490.558
1tktH12Gag-Pol polyprotein2.7.7.490.554
1tkzH16Gag-Pol polyprotein2.7.7.490.549
1s9eADBGag-Pol polyprotein2.7.7.490.547
3megT27Gag-Pol polyprotein2.7.7.490.547
1ikwEFZGag-Pol polyprotein2.7.7.490.545
3med65BGag-Pol polyprotein2.7.7.490.540
1revTB9Gag-Pol polyprotein2.7.7.490.537
1c1bGCAGag-Pol polyprotein2.7.7.490.533
4i2pG73Gag-Pol polyprotein2.7.7.490.533
4ifvT27Gag-Pol polyprotein2.7.7.490.532
2zd1T27Gag-Pol polyprotein2.7.7.490.531
4g1qT27Gag-Pol polyprotein2.7.7.490.530
2vg7NNIGag-Pol polyprotein2.7.7.490.529
3meeT27Gag-Pol polyprotein2.7.7.490.529
3qlhT27Gag-Pol polyprotein2.7.7.490.529
1rt5UC2Gag-Pol polyprotein2.7.7.490.528
3nbpJGZGag-Pol polyprotein2.7.7.490.528
1hpzAAPGag-Pol polyprotein2.7.7.490.527
3m8p65BGag-Pol polyprotein2.7.7.490.526
4id5T27Gag-Pol polyprotein2.7.7.490.524
1hnvTBOGag-Pol polyprotein2.7.7.490.523
1s6qTPBGag-Pol polyprotein2.7.7.490.523
1tkxGWBGag-Pol polyprotein2.7.7.490.522
4kko1REGag-Pol polyprotein2.7.7.490.519
1s1wUC1Gag-Pol polyprotein2.7.7.490.515
3i0rRT3Gag-Pol polyprotein2.7.7.490.514
3m8qDJZGag-Pol polyprotein2.7.7.490.512
1ikvEFZGag-Pol polyprotein2.7.7.490.511
1rt7UC4Gag-Pol polyprotein2.7.7.490.509
4i2q1BTGag-Pol polyprotein2.7.7.490.508
4ko0JLJGag-Pol polyprotein2.7.7.490.506
1hniAAAGag-Pol polyprotein2.7.7.490.505
4ig3T27Gag-Pol polyprotein2.7.7.490.505
1hquHBYGag-Pol polyprotein2.7.7.490.501
2opsHBQGag-Pol polyprotein2.7.7.490.500
1tvrTB9Gag-Pol polyprotein2.7.7.490.499
2opqHBQGag-Pol polyprotein2.7.7.490.499
1rt2TNKGag-Pol polyprotein2.7.7.490.498
2hndNVPGag-Pol polyprotein2.7.7.490.498
3mec65BGag-Pol polyprotein2.7.7.490.498
3dmjGWEPol protein/0.497
3i0sRT7Gag-Pol polyprotein2.7.7.490.497
4i7fNVEGag-Pol polyprotein2.7.7.490.497
3lanKBTGag-Pol polyprotein2.7.7.490.496
1fk9EFZGag-Pol polyprotein2.7.7.490.495
4rw6494Gag-Pol polyprotein2.7.7.490.494
2rf2MRXGag-Pol polyprotein2.7.7.490.493
3dleGFAGag-Pol polyprotein2.7.7.490.493
1eetBFUGag-Pol polyprotein2.7.7.490.492
1jlcFTCGag-Pol polyprotein2.7.7.490.492
3irxUDRGag-Pol polyprotein2.7.7.490.490
1jlqSBNGag-Pol polyprotein2.7.7.490.488
3bgrT27Gag-Pol polyprotein2.7.7.490.487
1rt1MKCGag-Pol polyprotein2.7.7.490.484
3ffi3OBGag-Pol polyprotein2.7.7.490.484
2ban357Gag-Pol polyprotein2.7.7.490.481
4kfbT27Gag-Pol polyprotein2.7.7.490.481
5uviZMAAdenosine receptor A2a/0.480
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.479
1c1c612Gag-Pol polyprotein2.7.7.490.478
1s1tUC1Gag-Pol polyprotein2.7.7.490.477
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.474
2vg5NNCGag-Pol polyprotein2.7.7.490.472
3gc9B45Mitogen-activated protein kinase 112.7.11.240.472
5cyqT27Gag-Pol polyprotein2.7.7.490.471
3lalKRVGag-Pol polyprotein2.7.7.490.468
3t1a5MAGag-Pol polyprotein2.7.7.490.468
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.466
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.464
2a4zBYMPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.463
3h0a9RARetinoic acid receptor RXR-alpha/0.463
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.463
1klmSPPGag-Pol polyprotein2.7.7.490.461
2oppHBQGag-Pol polyprotein2.7.7.490.461
3lfcZ86Mitogen-activated protein kinase 14/0.461
4o71CPBBromodomain-containing protein 4/0.460
1v7aFRCAdenosine deaminase3.5.4.40.459
1jlgUC1Gag-Pol polyprotein2.7.7.490.458
2vcmM11Isopenicillin N synthase1.21.3.10.458
3zkyWT4Isopenicillin N synthase1.21.3.10.458
5k2aZMAAdenosine receptor A2a/0.458
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.457
5k2bZMAAdenosine receptor A2a/0.457
1zidZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.456
2y60M8FIsopenicillin N synthase1.21.3.10.455
3c6uM22Gag-Pol polyprotein2.7.7.490.455
3s7a684Dihydrofolate reductase1.5.1.30.454
4f1sF1SPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
2wotZZGTGF-beta receptor type-12.7.11.300.453
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.453
3nx4NAPPutative oxidoreductase/0.453
3v8w0G2Tyrosine-protein kinase ITK/TSK2.7.10.20.453
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
1l2jETCEstrogen receptor beta/0.452
2c3qGTXGlutathione S-transferase theta-12.5.1.180.452
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.452
5k2cZMAAdenosine receptor A2a/0.452
5jtbZMAAdenosine receptor A2a/0.452
1bk0ACVIsopenicillin N synthase1.21.3.10.451
2vssACOHydroxycinnamoyl-CoA hydratase-lyase4.1.2.410.451
2xvv9DNSerum albumin/0.451
3lj3WYEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
3s79ASDAromatase1.14.14.140.451
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.451
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.451
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
3b9lAZZSerum albumin/0.450
3zoiM2WIsopenicillin N synthase1.21.3.10.450
1fkoEFZGag-Pol polyprotein2.7.7.490.449
1uzwCDHIsopenicillin N synthase1.21.3.10.449
5d7pOCZNAD-dependent protein deacetylase sirtuin-23.5.10.449
1a4iNDPC-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.448
2hw2RFPRifampin ADP-ribosyl transferase/0.448
2vbpVB1Isopenicillin N synthase1.21.3.10.448
3mfuANPPeripheral plasma membrane protein CASK2.7.11.10.448
4em9TCEPeroxisome proliferator-activated receptor gamma/0.448
4h380YXDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.448
3emlZMAAdenosine receptor A2a/0.448
1jpaANPEphrin type-B receptor 22.7.10.10.447
1o5rFR9Adenosine deaminase3.5.4.40.447
2bilBI1Serine/threonine-protein kinase pim-12.7.11.10.447
2y46MIVMycinamicin IV hydroxylase/epoxidase/0.447
2yee2ECHeat shock protein HSP 90-alpha/0.447
5k2dZMAAdenosine receptor A2a/0.447
1oc1ASVIsopenicillin N synthase1.21.3.10.446
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
3ctj320Hepatocyte growth factor receptor2.7.10.10.446
2nv6ZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
4j6cSTRCytochrome P450 monooxygenase/0.445
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.445
4ucnMYAGlycylpeptide N-tetradecanoyltransferase/0.445
1oguST8Cyclin-dependent kinase 22.7.11.220.444
1zgaHMKIsoflavone 4'-O-methyltransferase/0.444
2zv2609Calcium/calmodulin-dependent protein kinase kinase 22.7.11.170.444
3pqbVGPPutative oxidoreductase/0.444
4imoPWZProstaglandin-H2 D-isomerase5.3.99.20.444
5iua6DXAdenosine receptor A2a/0.444
1yinCM3Estrogen receptor/0.443
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
2z97CAMCamphor 5-monooxygenase1.14.15.10.443
2zjwREFCasein kinase II subunit alpha2.7.11.10.443
3cgdCOACoenzyme A disulfide reductase/0.443
4hnc0UTMandelate racemase/0.443
4j03FVSBifunctional epoxide hydrolase 23.1.3.760.443
1hvyD16Thymidylate synthase2.1.1.450.442
1n4hREANuclear receptor ROR-beta/0.442
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
2iviACWIsopenicillin N synthase1.21.3.10.442
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
3s3vTOPDihydrofolate reductase1.5.1.30.442
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4a81DXCMajor pollen allergen Bet v 1-A/0.442
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4iae1DXAlr2278 protein/0.442
4rw4494Gag-Pol polyprotein2.7.7.490.442
1qxlFR8Adenosine deaminase3.5.4.40.441
2bxmIMNSerum albumin/0.441
2ph5NADHomospermidine synthase/0.441
2ykeYKEHeat shock protein HSP 90-alpha/0.441
3w0yDS4Vitamin D3 receptor/0.441
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
4hfmNAP2-alkenal reductase (NADP(+)-dependent)/0.441
1qjfACSIsopenicillin N synthase1.21.3.10.440
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.440
3h1jSMACytochrome b/0.440
5bp9SAHPutative methyltransferase protein/0.440