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 |
|---|---|---|---|
| 2v95 | HCY | Corticosteroid-binding globulin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2v95 | HCY | Corticosteroid-binding globulin | / | 1.000 | |
| 2vdy | HCY | Corticosteroid-binding globulin | / | 0.521 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.515 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.513 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.499 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.498 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.495 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.492 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.489 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.488 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.488 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.485 | |
| 1pr0 | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.483 | |
| 1rfq | LAR | Actin, alpha skeletal muscle | / | 0.483 | |
| 4c49 | HCY | Corticosteroid-binding globulin | / | 0.481 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.479 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.478 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.478 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.475 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.472 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.471 | |
| 1pke | 2FD | Purine nucleoside phosphorylase DeoD-type | / | 0.470 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.470 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.470 | |
| 4x81 | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.470 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.468 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.467 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.466 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.463 | |
| 3bl7 | DD1 | m7GpppX diphosphatase | 3.6.1.59 | 0.462 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.460 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.460 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.459 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.459 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.459 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.459 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.459 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.458 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.458 | |
| 1zdw | FLV | Prenyltransferase | / | 0.458 | |
| 4isg | 1FY | Glucokinase | 2.7.1.2 | 0.458 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.457 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.457 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.457 | |
| 2plm | SIB | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | 3.5.4.28 | 0.456 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.456 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.456 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.455 | |
| 3uaw | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.455 | |
| 4ise | 1FW | Glucokinase | 2.7.1.2 | 0.455 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 1k9s | FM1 | Purine nucleoside phosphorylase DeoD-type | / | 0.453 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.453 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.453 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.453 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.453 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.453 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.452 | |
| 1pfy | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.452 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.452 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.452 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.452 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.452 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.451 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.451 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.451 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.450 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.450 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.450 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.450 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.449 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.448 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.448 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.448 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.448 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2yye | APC | Selenide, water dikinase | 2.7.9.3 | 0.448 | |
| 1k9s | FM2 | Purine nucleoside phosphorylase DeoD-type | / | 0.447 | |
| 1nqw | 5YL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 1pr6 | XYA | Purine nucleoside phosphorylase DeoD-type | / | 0.447 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.447 | |
| 2v9j | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.447 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.447 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 4isu | IKM | Glutamate receptor 2 | / | 0.447 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.447 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.446 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 1k4g | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.446 | |
| 1pr5 | TBN | Purine nucleoside phosphorylase DeoD-type | / | 0.446 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.446 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.446 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.446 | |
| 3pbl | ETQ | D(3) dopamine receptor | / | 0.446 | |
| 2i4t | UA2 | Purine nucleoside phosphorylase, putative | / | 0.445 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.445 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.445 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.445 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.445 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.444 | |
| 1pr1 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.444 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.444 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4e0u | 0MV | Cyclic dipeptide N-prenyltransferase | / | 0.444 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.444 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.443 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.443 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2ywv | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | / | 0.443 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 4k39 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.443 | |
| 4ts9 | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.443 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.442 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.442 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3e7m | AT2 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.442 | |
| 4k5d | 1Q6 | Nitric oxide synthase, brain | 1.14.13.39 | 0.442 | |
| 4x7w | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.442 | |
| 1vhz | APR | ADP compounds hydrolase NudE | 3.6.1 | 0.441 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.441 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 5d7q | 4I5 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.441 | |
| 1a69 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.440 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.440 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.440 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.440 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 4ffl | ADP | Uncharacterized protein | / | 0.440 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.440 |