sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3cfo | GMP | DNA-directed DNA polymerase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3cfo | GMP | DNA-directed DNA polymerase | / | 1.000 | |
| 1clq | GDP | DNA-directed DNA polymerase | / | 0.610 | |
| 4i9q | XG4 | DNA-directed DNA polymerase | / | 0.601 | |
| 1waj | 5GP | DNA-directed DNA polymerase | / | 0.590 | |
| 4khn | XG4 | DNA-directed DNA polymerase | / | 0.554 | |
| 1ih7 | GMP | DNA-directed DNA polymerase | / | 0.553 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.501 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.483 | |
| 2v8p | CDP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.482 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.480 | |
| 1k4g | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.478 | |
| 4a16 | H34 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.471 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.471 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.471 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.471 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.470 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.469 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.469 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.466 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.466 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.466 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.465 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.465 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.464 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.464 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.464 | |
| 1f3e | DPZ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.463 | |
| 1isg | AGS | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 | 3.2.2.6 | 0.463 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.463 | |
| 1e2j | THM | Thymidine kinase | / | 0.462 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.462 | |
| 1pxg | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.461 | |
| 1wm1 | PTB | Proline iminopeptidase | 3.4.11.5 | 0.461 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.461 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1qk3 | 5GP | Hypoxanthine-guanine-xanthine phosphoribosyltransferase | 2.4.2.22 | 0.460 | |
| 3cr0 | 809 | Wee1-like protein kinase | 2.7.10.2 | 0.460 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.460 | |
| 4to2 | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.460 | |
| 2v2v | V12 | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.459 | |
| 2xk6 | EQH | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.459 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.459 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.459 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 1e6z | NGO | Chitinase | / | 0.458 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.458 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.458 | |
| 3c3e | FO1 | 2-phospho-L-lactate transferase | / | 0.458 | |
| 3l7g | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.457 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.457 | |
| 1x8b | 824 | Wee1-like protein kinase | 2.7.10.2 | 0.456 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.456 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.456 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.455 | |
| 3lpf | Z77 | Beta-glucuronidase | 3.2.1.31 | 0.455 | |
| 4dxl | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.455 | |
| 4i9z | 5BA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.455 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.454 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.454 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.454 | |
| 4bdr | KAI | Glutamate receptor ionotropic, kainate 2 | / | 0.454 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 3o9p | MHI | Periplasmic murein peptide-binding protein | / | 0.453 | |
| 4feu | 537 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.453 | |
| 4g8j | THM | Uridine phosphorylase | / | 0.453 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.452 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 2olc | ADP | Methylthioribose kinase | 2.7.1.100 | 0.452 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.451 | |
| 1ot3 | THM | Deoxynucleoside kinase | / | 0.451 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.451 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.451 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.451 | |
| 3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4rp8 | ASC | Ascorbate-specific PTS system EIIC component | / | 0.451 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.450 | |
| 1uwh | BAX | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.450 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.450 | |
| 2xkd | T3M | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.450 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.450 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 2xkf | BX1 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.449 | |
| 2z2w | 770 | Wee1-like protein kinase | 2.7.10.2 | 0.449 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.449 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.449 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.449 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3lfz | ADP | Uncharacterized protein MJ1225 | / | 0.449 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.449 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 4l0o | PLP | Cystathionine gamma-synthase | 2.5.1.48 | 0.449 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2v0u | FMN | NPH1-1 | / | 0.448 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.448 | |
| 4gh1 | 0WX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.448 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 4lcw | 1VY | Major histocompatibility complex class I-related gene protein | / | 0.448 | |
| 4rxp | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.448 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.447 | |
| 1g7v | PAI | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.447 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.447 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.447 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2g1a | 5HG | Class B acid phosphatase | 3.1.3.2 | 0.446 | |
| 2ojg | 19A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.446 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.446 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1ozq | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.445 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2fjm | 073 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.445 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4ajg | F07 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4gh3 | 0EV | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.445 | |
| 1lbb | KAI | Glutamate receptor 2 | / | 0.444 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.444 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.444 | |
| 3lpg | Z78 | Beta-glucuronidase | 3.2.1.31 | 0.444 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.444 | |
| 3u8d | U8D | Phospholipase A2, membrane associated | / | 0.444 | |
| 4d6q | PD2 | Lysine-specific demethylase 4D | 1.14.11 | 0.444 | |
| 4kxj | P34 | Nucleoprotein | / | 0.444 | |
| 4pjj | ADP | Unconventional myosin-VI | / | 0.444 | |
| 5fe1 | 12Q | Histone acetyltransferase KAT2B | 2.3.1.48 | 0.444 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 2r6j | NDP | Eugenol synthase 1 | 1.1.1.318 | 0.443 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.443 | |
| 3cqe | P91 | Wee1-like protein kinase | 2.7.10.2 | 0.443 | |
| 3i28 | 34N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.443 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.443 | |
| 1nd5 | 2BF | Prostatic acid phosphatase | 3.1.3.2 | 0.442 | |
| 1rxj | BNI | Streptavidin | / | 0.442 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 2z1w | BDI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.442 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.442 | |
| 3c4h | DRL | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 3e3u | NVC | Peptide deformylase | 3.5.1.88 | 0.442 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.442 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.441 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 2a5c | 8DA | Avidin | / | 0.441 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2mm3 | GCH | Gastrotropin | / | 0.441 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 5e9e | ANP | Myosin heavy chain kinase A | 2.7.11.7 | 0.441 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 1sjw | NGV | Nogalonic acid methyl ester cyclase | / | 0.440 | |
| 2b82 | ADN | Class B acid phosphatase | 3.1.3.2 | 0.440 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 2rku | R78 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.440 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2zoz | ET | Transcriptional regulator | / | 0.440 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3k45 | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3klb | FMN | Uncharacterized protein | / | 0.440 | |
| 3oji | PYV | Abscisic acid receptor PYL3 | / | 0.440 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 | |
| 4ec3 | REN | Reticuline oxidase | 1.21.3.3 | 0.440 | |
| 4g2w | NI0 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.440 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 5erm | 210 | Fusicoccadiene synthase | 4.2.3.43 | 0.440 |