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 |
---|---|---|---|
1w2g | THM | Thymidylate kinase | 2.7.4.9 |
PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
---|---|---|---|---|---|
1w2g | THM | Thymidylate kinase | 2.7.4.9 | 1.000 | |
1n5i | TMP | Thymidylate kinase | 2.7.4.9 | 0.572 | |
1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.506 | |
4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.501 | |
3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.496 | |
2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.495 | |
2rd6 | 78P | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.494 | |
1kl2 | FON | Serine hydroxymethyltransferase | / | 0.492 | |
4xba | 5GP | Aprataxin-like protein | 3 | 0.490 | |
1ndy | FR3 | Adenosine deaminase | 3.5.4.4 | 0.488 | |
2j7c | IDE | Beta-glucosidase A | 3.2.1.21 | 0.488 | |
3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.488 | |
2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.486 | |
2r7n | ADP | 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase | / | 0.484 | |
3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.483 | |
4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.483 | |
1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.480 | |
5aqz | SGV | Heat shock 70 kDa protein 1A | / | 0.480 | |
3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.478 | |
3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.478 | |
1j7l | ADP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.476 | |
5k2c | ZMA | Adenosine receptor A2a | / | 0.476 | |
2pbz | ATP | Uncharacterized protein | / | 0.475 | |
2v34 | CTN | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.475 | |
3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.472 | |
1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
3fow | IMH | Purine nucleoside phosphorylase | / | 0.471 | |
3six | GDP | Nodulation protein Z | / | 0.471 | |
2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.470 | |
3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.470 | |
3e5a | VX6 | Aurora kinase A | 2.7.11.1 | 0.470 | |
1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.469 | |
2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.469 | |
3sfy | 3FY | Uncharacterized protein | / | 0.469 | |
1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.468 | |
2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.467 | |
3gwu | SRE | Na(+):neurotransmitter symporter (Snf family) | / | 0.467 | |
2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.466 | |
4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.465 | |
1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.464 | |
1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.464 | |
2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.464 | |
3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.463 | |
4kxl | 6C6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 0.463 | |
1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.462 | |
2zse | ACP | Pantothenate kinase | 2.7.1.33 | 0.462 | |
3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.462 | |
4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.462 | |
4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.461 | |
1jdz | FMB | Purine nucleoside phosphorylase | / | 0.461 | |
4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.460 | |
1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
3oxk | 5GP | Histidine triad nucleotide-binding protein | 3 | 0.460 | |
3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.460 | |
4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.460 | |
5ccy | TMP | Polymerase acidic protein | / | 0.460 | |
3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.459 | |
3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
4c1f | X8Z | Metallo-beta-lactamase type 2 | / | 0.459 | |
5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.459 | |
2r0c | FAD | Putative FAD-monooxygenase | / | 0.458 | |
3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.458 | |
3mcy | ZH1 | FimH | / | 0.458 | |
4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.458 | |
2iea | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.457 | |
2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
2yoh | WMJ | Thymidylate kinase | / | 0.457 | |
3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.457 | |
3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.457 | |
1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
3q8u | ADP | Nucleoside diphosphate kinase | / | 0.456 | |
3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.456 | |
5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.456 | |
2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.455 | |
3fnl | SHA | Lactoperoxidase | / | 0.455 | |
4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.455 | |
4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.455 | |
1e2n | RCA | Thymidine kinase | / | 0.454 | |
1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.454 | |
1uk1 | FRQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.454 | |
2g26 | 3LG | Renin | 3.4.23.15 | 0.454 | |
3hiy | UTP | Uncharacterized protein | / | 0.454 | |
4m48 | 21B | Sodium-dependent dopamine transporter | / | 0.454 | |
4xnw | 2ID | P2Y purinoceptor 1 | / | 0.454 | |
1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.453 | |
2yof | 74W | Thymidylate kinase | / | 0.453 | |
4lv5 | ADP | Rhoptry protein 5B | / | 0.453 | |
1mew | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.452 | |
4y6u | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.452 | |
1pke | 2FD | Purine nucleoside phosphorylase DeoD-type | / | 0.451 | |
3vg9 | ZMA | Adenosine receptor A2a | / | 0.451 | |
4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.451 | |
4mka | 2AY | Genome polyprotein | 2.7.7.48 | 0.451 | |
1k9s | FM1 | Purine nucleoside phosphorylase DeoD-type | / | 0.450 | |
2wba | FAD | Trypanothione reductase | 1.8.1.12 | 0.450 | |
3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
3c34 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.450 | |
3dqr | JI2 | Nitric oxide synthase, brain | 1.14.13.39 | 0.450 | |
3ebi | BEY | M1 family aminopeptidase | 3.4.11 | 0.450 | |
3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.450 | |
3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.450 | |
3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.450 | |
4aza | MGO | Eukaryotic translation initiation factor 4E | / | 0.450 | |
4gxs | 0YS | Glutamate receptor 2 | / | 0.450 | |
4ug7 | 1EV | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.450 | |
1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.449 | |
1hk5 | T44 | Serum albumin | / | 0.449 | |
1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.449 | |
1ryd | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.449 | |
1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.449 | |
3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.449 | |
4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.449 | |
1g8o | U5P | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.448 | |
2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.448 | |
2e93 | B29 | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.448 | |
2zdg | ADP | D-alanine--D-alanine ligase | / | 0.448 | |
3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
3zei | AWH | O-acetylserine sulfhydrylase | / | 0.448 | |
4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.448 | |
1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.447 | |
1kru | IPT | Galactoside O-acetyltransferase | 2.3.1.18 | 0.447 | |
1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.447 | |
1r2j | FAD | FkbI | / | 0.447 | |
2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
2nom | DUT | Poly(A) polymerase, putative | / | 0.447 | |
2vrj | NCW | Beta-glucosidase A | 3.2.1.21 | 0.447 | |
3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
4h6p | FMN | Chromate reductase | / | 0.447 | |
4kf1 | HT5 | Aryldialkylphosphatase | 3.1.8.1 | 0.447 | |
4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.447 | |
1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
2qs1 | UB1 | Glutamate receptor ionotropic, kainate 1 | / | 0.446 | |
3hbf | MYC | Flavonoid 3-O-glucosyltransferase | 2.4.1 | 0.446 | |
4gd9 | BTN | Streptavidin | / | 0.446 | |
4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.446 | |
4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.446 | |
4qem | HC4 | Phospholipase A2 VRV-PL-VIIIa | / | 0.446 | |
5k2a | ZMA | Adenosine receptor A2a | / | 0.446 | |
1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.445 | |
2hq9 | FAD | Mll6688 protein | / | 0.445 | |
2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.445 | |
2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.445 | |
3bgx | TMP | Thymidylate synthase | / | 0.445 | |
3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.445 | |
3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.445 | |
4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.445 | |
5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.445 | |
1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.444 | |
1uk0 | FRM | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.444 | |
2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.444 | |
2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
3ggc | H26 | Hypoxanthine-guanine phosphoribosyltransferase | 2.4.2.8 | 0.444 | |
3tza | TZG | Glutamate receptor 2 | / | 0.444 | |
4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.444 | |
4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
4fhp | UTP | Terminal uridylyltransferase cid1 | / | 0.444 | |
4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
5k2d | ZMA | Adenosine receptor A2a | / | 0.444 | |
1pg2 | ADN | Methionine--tRNA ligase | 6.1.1.10 | 0.443 | |
2bra | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.443 | |
2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
2p5u | NAD | UDP-glucose 4-epimerase | / | 0.443 | |
2zsc | BTN | Tamavidin2 | / | 0.443 | |
3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.443 | |
3hu1 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.443 | |
3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.443 | |
3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
3tda | PN0 | Cytochrome P450 2D6 | / | 0.443 | |
3uk6 | ADP | RuvB-like 2 | 3.6.4.12 | 0.443 | |
1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.442 | |
1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.442 | |
1zdw | FLV | Prenyltransferase | / | 0.442 | |
4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.442 | |
4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
4gki | 0JN | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.442 | |
4r5w | XAV | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
1dnp | MHF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
1l8a | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
1y56 | FMN | Uncharacterized protein | / | 0.441 | |
1y56 | FMN | 382aa long hypothetical sarcosine oxidase | / | 0.441 | |
1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.441 | |
3q7f | ED2 | Uncharacterized protein | / | 0.441 | |
3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.441 | |
3w5u | FAD | Ferredoxin | / | 0.441 | |
4gn6 | TYL | Lactoperoxidase | 1.11.1.7 | 0.441 | |
4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.441 | |
5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.441 | |
1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.440 | |
1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.440 | |
1kwc | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.440 | |
1swe | BTN | Streptavidin | / | 0.440 | |
1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
2gqf | FAD | Uncharacterized protein HI_0933 | / | 0.440 | |
2vi5 | Y19 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
3dej | RXC | Caspase-3 | 3.4.22.56 | 0.440 | |
3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.440 | |
4bjb | P34 | Tankyrase-2 | 2.4.2.30 | 0.440 | |
4kc2 | WS2 | Histo-blood group ABO system transferase | / | 0.440 | |
4rxq | DUT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.440 | |
4xp4 | COC | Sodium-dependent dopamine transporter | / | 0.440 | |
4zob | LGC | Lin1840 protein | / | 0.440 | |
5dn1 | AMZ | Phosphoribosyl isomerase A | 5.3.1.16 | 0.440 |