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 |
|---|---|---|---|
| 5aun | ADP | Iron-sulfur cluster carrier protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5aun | ADP | Iron-sulfur cluster carrier protein | / | 1.000 | |
| 4beb | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.494 | |
| 3m0e | ATP | Transcriptional regulator (NtrC family) | / | 0.491 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.484 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.483 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.481 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.480 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.480 | |
| 2bfy | H1N | Aurora kinase B-A | 2.7.11.1 | 0.477 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.475 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.473 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.470 | |
| 1uyc | PU7 | Heat shock protein HSP 90-alpha | / | 0.469 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.467 | |
| 3zw3 | ZW3 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.467 | |
| 4n6h | EJ4 | Delta-type opioid receptor | / | 0.467 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.466 | |
| 2o12 | FMN | Chorismate synthase | / | 0.466 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.464 | |
| 4xvr | GNP | GTPase HRas | / | 0.464 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.463 | |
| 2o2q | NAP | Cytosolic 10-formyltetrahydrofolate dehydrogenase | 1.5.1.6 | 0.463 | |
| 3qk0 | QK0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.463 | |
| 3zcw | 4A2 | Kinesin-like protein KIF11 | / | 0.463 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.463 | |
| 5iqa | GNP | Bifunctional AAC/APH | 2.3.1 | 0.463 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.462 | |
| 4ful | 0VU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 2fwy | H64 | Heat shock protein HSP 90-alpha | / | 0.460 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.459 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.459 | |
| 4be7 | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.459 | |
| 4ffl | ADP | Uncharacterized protein | / | 0.459 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.459 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.459 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.458 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.458 | |
| 2xrw | ANP | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.458 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 3mtf | A3F | Activin receptor type-1 | 2.7.11.30 | 0.458 | |
| 1ie4 | T44 | Transthyretin | / | 0.457 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 2iut | AGS | DNA translocase FtsK | / | 0.457 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.457 | |
| 4yaf | 2AM | NADPH--cytochrome P450 reductase | / | 0.457 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.456 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.456 | |
| 3vth | APC | Carbamoyltransferase | / | 0.456 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.455 | |
| 3hu2 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.455 | |
| 3o0i | P54 | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.455 | |
| 1zhw | HC2 | Oxysterol-binding protein homolog 4 | / | 0.454 | |
| 2a5y | ATP | Cell death protein 4 | / | 0.454 | |
| 2hy0 | 306 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.454 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.454 | |
| 2jiz | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.453 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.453 | |
| 4fsm | HK1 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.453 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.453 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 2a4z | BYM | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 2yis | YIS | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 4bbh | NHW | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4e03 | ADP | Plasmid partitioning protein ParF | / | 0.452 | |
| 4ezk | 0SD | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.452 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.452 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.452 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.451 | |
| 4gvj | ADP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.451 | |
| 4nyi | GNP | GTPase HRas | / | 0.451 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3hll | I45 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 3inm | NDP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.450 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.450 | |
| 1mab | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.449 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.449 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.449 | |
| 1qax | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.448 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.448 | |
| 1wuu | ANP | Galactokinase | 2.7.1.6 | 0.448 | |
| 2oby | NAP | Quinone oxidoreductase PIG3 | 1 | 0.448 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 4wuc | ANP | DNA gyrase subunit B | / | 0.448 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1ijj | ATP | Actin, alpha skeletal muscle | / | 0.447 | |
| 1sn0 | T44 | Transthyretin | / | 0.447 | |
| 2h8h | H8H | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.447 | |
| 2qoq | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.447 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.447 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.447 | |
| 3hu1 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.447 | |
| 3nnu | EDB | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3stu | DK3 | Methylketone synthase I | / | 0.447 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.447 | |
| 3w0s | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.447 | |
| 4c59 | FEF | Cyclin-G-associated kinase | 2.7.11.1 | 0.447 | |
| 4fdn | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.447 | |
| 4l9q | 9TP | Serum albumin | / | 0.447 | |
| 4ydu | ADP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.447 | |
| 1jut | LYD | Thymidylate synthase | / | 0.446 | |
| 1osv | CHC | Bile acid receptor | / | 0.446 | |
| 2cah | NDP | Catalase | 1.11.1.6 | 0.446 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.446 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.446 | |
| 2jj2 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.446 | |
| 2oye | IM8 | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.446 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 3cgb | COA | Coenzyme A disulfide reductase | / | 0.446 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 3qfs | NAP | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 3ruq | ADP | Chaperonin | / | 0.446 | |
| 3v5j | 0F2 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.446 | |
| 4bec | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.446 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.446 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.446 | |
| 4xey | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.446 | |
| 1jm6 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.445 | |
| 1zio | AP5 | Adenylate kinase | / | 0.445 | |
| 2b0m | 201 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.445 | |
| 2iyg | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.445 | |
| 2j14 | GNI | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 2q97 | ATP | Actin, alpha skeletal muscle | / | 0.445 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.445 | |
| 3ojx | NAP | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.445 | |
| 4a33 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4btm | F8E | Tau-tubulin kinase 1 | 2.7.11.1 | 0.445 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.445 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4jbp | YPH | Aurora kinase A | 2.7.11.1 | 0.445 | |
| 4mxx | DB8 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.445 | |
| 5ack | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.445 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.445 | |
| 1hop | GCP | Adenylosuccinate synthetase | / | 0.444 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.444 | |
| 1pox | FAD | Pyruvate oxidase | 1.2.3.3 | 0.444 | |
| 1qkn | RAL | Estrogen receptor beta | / | 0.444 | |
| 1t44 | ATP | Actin, alpha skeletal muscle | / | 0.444 | |
| 2xvw | 9NR | Serum albumin | / | 0.444 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.444 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.444 | |
| 3zlx | 5EZ | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.444 | |
| 4jia | 1K3 | Tyrosine-protein kinase JAK2 | / | 0.444 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.444 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.443 | |
| 1sn5 | T3 | Transthyretin | / | 0.443 | |
| 2j0l | ANP | Focal adhesion kinase 1 | 2.7.10.2 | 0.443 | |
| 2wsa | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 2xne | ASH | Aurora kinase A | 2.7.11.1 | 0.443 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.443 | |
| 3dzd | ADP | Transcriptional regulator (NtrC family) | / | 0.443 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.443 | |
| 3fzp | AGS | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.443 | |
| 3kvx | FMY | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.443 | |
| 3oro | AGS | Serine/threonine protein kinase | / | 0.443 | |
| 3otq | MZL | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.443 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.443 | |
| 4okt | 198 | Androgen receptor | / | 0.443 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.443 | |
| 1mb9 | ATP | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.442 | |
| 1nsf | ATP | Vesicle-fusing ATPase | 3.6.4.6 | 0.442 | |
| 2j0m | 4ST | Focal adhesion kinase 1 | 2.7.10.2 | 0.442 | |
| 2ywv | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | / | 0.442 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.442 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.442 | |
| 3q7d | NPX | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.442 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.442 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4c4f | 7CE | Dual specificity protein kinase TTK | 2.7.12.1 | 0.442 | |
| 4pl8 | ATP | Actin, alpha skeletal muscle | / | 0.442 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.442 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.442 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.442 | |
| 1jqh | ANP | Insulin-like growth factor 1 receptor | 2.7.10.1 | 0.441 | |
| 1sgu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.441 | |
| 2ceo | T44 | Thyroxine-binding globulin | / | 0.441 | |
| 2pun | ACP | Methylthioribose kinase | 2.7.1.100 | 0.441 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.441 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.441 | |
| 2yjx | YJX | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.441 | |
| 3ls8 | AJZ | Phosphatidylinositol 3-kinase catalytic subunit type 3 | 2.7.1.137 | 0.441 | |
| 3nc9 | TR3 | Ketohexokinase | / | 0.441 | |
| 3qfr | NAP | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 3qft | NAP | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 3uqd | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.441 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.441 | |
| 4ffr | ATP | Uncharacterized protein | / | 0.441 | |
| 4fz7 | 0VH | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.441 | |
| 4ixf | IXF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4kcf | AKM | FAD-dependent oxidoreductase | / | 0.441 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.441 | |
| 5dnr | ATP | Aurora kinase A | 2.7.11.1 | 0.441 | |
| 5iw5 | NMN | NADH pyrophosphatase | / | 0.441 | |
| 1b38 | ATP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1ht2 | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.440 | |
| 1kgj | FL8 | Transthyretin | / | 0.440 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.440 | |
| 2bdf | 24A | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.440 | |
| 2gnh | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.440 | |
| 2vrx | 447 | Aurora kinase B-A | 2.7.11.1 | 0.440 | |
| 2wqb | QQ1 | Angiopoietin-1 receptor | 2.7.10.1 | 0.440 | |
| 2yfe | YFE | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3bxz | ADP | Protein translocase subunit SecA | / | 0.440 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.440 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3opd | HIE | Heat shock protein 83 | / | 0.440 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.440 | |
| 3wdl | ATP | 4-phosphopantoate--beta-alanine ligase | 6.3.2.36 | 0.440 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.440 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.440 | |
| 5cb5 | APR | O-acetyl-ADP-ribose deacetylase | / | 0.440 | |
| 5eox | ADP | Type 4 fimbrial biogenesis protein PilM | / | 0.440 |