sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 5htp | ANP | Probable sugar kinase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5htp | ANP | Probable sugar kinase | / | 1.000 | |
| 5htx | ADP | Putative xylulose kinase | / | 0.562 | |
| 2xf0 | 4UB | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.479 | |
| 1w8c | N69 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.478 | |
| 4y9q | C2E | Uncharacterized protein | / | 0.474 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.472 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.471 | |
| 4u9a | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.471 | |
| 1ep3 | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit | / | 0.470 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.470 | |
| 4ez5 | 0RS | Cyclin-dependent kinase 6 | 2.7.11.22 | 0.470 | |
| 2wip | P49 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.469 | |
| 1ea0 | FMN | Glutamate synthase [NADPH] large chain | 1.4.1.13 | 0.468 | |
| 3qvx | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.468 | |
| 1gih | 1PU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.467 | |
| 3uzp | 0CK | Casein kinase I isoform delta | 2.7.11.1 | 0.467 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.466 | |
| 4jlc | SU6 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.466 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.466 | |
| 3tkh | 07S | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.465 | |
| 4ftk | H9K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.465 | |
| 2a0c | CK9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.463 | |
| 2acs | NAP | Aldose reductase | 1.1.1.21 | 0.463 | |
| 3ezv | EZV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.463 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.462 | |
| 2qhm | 7CS | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.461 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.461 | |
| 3tki | S25 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.461 | |
| 1k6v | XN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 2ayp | 43A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.460 | |
| 2c3k | ABO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.460 | |
| 2exm | ZIP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.460 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.460 | |
| 3tnw | F18 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.460 | |
| 5dr9 | SKE | Aurora kinase A | 2.7.11.1 | 0.460 | |
| 5es7 | FON | Linear gramicidin synthase subunit A | / | 0.460 | |
| 3s2p | PMU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.459 | |
| 1jhr | P2P | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.458 | |
| 3i60 | E86 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.458 | |
| 2c6t | DT5 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.457 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.457 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 2hy0 | 306 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.456 | |
| 3lfq | A28 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.456 | |
| 4fnz | NZF | ALK tyrosine kinase receptor | 2.7.10.1 | 0.456 | |
| 4fsu | HK5 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.456 | |
| 4ftl | H0K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.456 | |
| 3qxp | X64 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.455 | |
| 1e1x | NW1 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.454 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.454 | |
| 2iw8 | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.454 | |
| 3nun | JMZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.454 | |
| 4fsq | HK3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.454 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 2vv9 | IM9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 3ama | SKE | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.453 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.453 | |
| 3pwr | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 4bcq | TJF | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.453 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.452 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.452 | |
| 2vtq | LZA | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.452 | |
| 3qcq | 3Q0 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.452 | |
| 4fsr | HKC | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.452 | |
| 4gmy | 0X5 | Tyrosine-protein kinase JAK2 | / | 0.452 | |
| 1fvt | 106 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.451 | |
| 1oiy | N41 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 1z5m | LI8 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.451 | |
| 2bro | DF2 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 2ym4 | 4YM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.451 | |
| 3rwp | ABQ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.451 | |
| 4bzo | 676 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.451 | |
| 4z87 | 5GP | Inosine-5'-monophosphate dehydrogenase | / | 0.451 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.450 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.450 | |
| 2f3k | RO1 | Protease | / | 0.450 | |
| 2iw9 | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 2pe1 | 517 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.450 | |
| 2vu3 | LZE | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 2w17 | I19 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 3fmh | 533 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 3o0g | 3O0 | Cyclin-dependent-like kinase 5 | 2.7.11.1 | 0.450 | |
| 3s1h | 56Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 3sc1 | 3S1 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.450 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.450 | |
| 4fkw | 62K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 1aq1 | STU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.449 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.449 | |
| 1nvq | UCN | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 1x98 | NAP | Aldose reductase | 1.1.1.21 | 0.449 | |
| 2brn | DF1 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.449 | |
| 2x8e | X8E | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.449 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.449 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.449 | |
| 3s4q | NK0 | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 4bdc | ODH | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.449 | |
| 4gh2 | HK0 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 4ktc | 1X3 | Genome polyprotein | 3.4.21.98 | 0.449 | |
| 1rkd | ADP | Ribokinase | / | 0.448 | |
| 2c6o | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2nnp | ROC | Protease | / | 0.448 | |
| 2q3k | MUW | Gag-Pol polyprotein | / | 0.448 | |
| 2w06 | FRV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 3el5 | 1UN | Gag-Pol polyprotein | / | 0.448 | |
| 3qd0 | 3Q4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 3s56 | ROC | Protease | / | 0.448 | |
| 4fkt | 48K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 4ft5 | H2K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 4lop | SB4 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 2hqp | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2ojj | 82A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.447 | |
| 2r5t | ANP | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.447 | |
| 2xa4 | AZ5 | Tyrosine-protein kinase JAK2 | / | 0.447 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.447 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.447 | |
| 3ruv | ANP | Chaperonin | / | 0.447 | |
| 4a9u | A9U | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.447 | |
| 4acm | 7YG | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.447 | |
| 4bi1 | ZO6 | Dual specificity protein kinase TTK | 2.7.12.1 | 0.447 | |
| 4ekl | 0RF | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.447 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.447 | |
| 4kik | KSA | Inhibitor of nuclear factor kappa-B kinase subunit beta | 2.7.11.10 | 0.447 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.447 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 3em6 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.446 | |
| 3qpj | N4I | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3r9d | X6B | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 3rak | 03Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 3zcs | CAW | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.446 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.446 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.445 | |
| 1h0w | 207 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 1ogu | ST8 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 1okz | UCN | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.445 | |
| 1qvn | FRI | Interleukin-2 | / | 0.445 | |
| 1w7h | 3IP | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.445 | |
| 2yek | EAM | Bromodomain-containing protein 2 | / | 0.445 | |
| 3ft5 | MO8 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 3kga | LX9 | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.445 | |
| 3lfn | A27 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 3nie | ANP | Mitogen-activated protein kinase | / | 0.445 | |
| 3ute | FAD | UDP-galactopyranose mutase | / | 0.445 | |
| 4ftm | 1HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 4qmp | DKI | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.445 | |
| 5dt0 | SKE | Aurora kinase A | 2.7.11.1 | 0.445 | |
| 2e9n | 76A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 2owk | SAH | Diphthine synthase | / | 0.444 | |
| 2y9q | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.444 | |
| 3ekt | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.444 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3r8l | Z30 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.444 | |
| 4fst | HK4 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.444 | |
| 5hsa | FAS | Alcohol oxidase 1 | 1.1.3.13 | 0.444 | |
| 1a9m | U0E | Gag-Pol polyprotein | / | 0.443 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.443 | |
| 2i40 | BLZ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 2vo7 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 2w05 | FRT | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3qro | NK9 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3sw7 | 19K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3uli | 1N3 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 4ft7 | H3K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.443 | |
| 1nvr | STU | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 1oi9 | N20 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.442 | |
| 2p2b | PRX | Acetyl-coenzyme A synthetase | / | 0.442 | |
| 2p2j | PRX | Acetyl-coenzyme A synthetase | / | 0.442 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 3krw | BA1 | Beta-adrenergic receptor kinase 1 | 2.7.11.15 | 0.442 | |
| 3ral | 04Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 3stw | 2TD | Methylketone synthase I | / | 0.442 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.442 | |
| 4ftr | 5HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 4hvg | 19Q | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.442 | |
| 4ks8 | B49 | Serine/threonine-protein kinase PAK 6 | 2.7.11.1 | 0.442 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.442 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.441 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.441 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3qqk | X02 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4bcm | T7Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 4eok | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 4fv1 | EK4 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.441 | |
| 4fx3 | 60K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 4g16 | 0VM | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.441 | |
| 4hyh | 1AM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.441 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.441 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.440 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.440 | |
| 2cem | 2AH | Pol protein | / | 0.440 | |
| 2hog | 710 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2hxq | 373 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.440 | |
| 2p2h | 994 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.440 | |
| 2qd7 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.440 | |
| 2uzb | C75 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 2wmu | ZYU | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2ylt | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 3o9g | F53 | Gag-Pol polyprotein | / | 0.440 | |
| 3qtr | X36 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 4ftc | H6K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 4ftq | 4HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 |