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 |
|---|---|---|---|
| 2zhw | 12U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.744 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.730 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.722 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.703 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.702 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.701 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.698 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.694 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.691 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.685 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.683 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.682 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.677 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.677 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.675 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.674 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.670 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.667 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.665 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.664 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.664 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.664 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.662 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.661 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.659 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.658 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.656 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.654 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.653 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.653 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.651 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.650 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.650 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.647 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.647 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.645 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.644 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.644 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.644 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.641 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.636 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.632 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.630 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.630 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.630 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.629 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.629 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.628 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.627 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.627 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.626 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.625 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.625 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.625 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.621 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.620 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.618 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.617 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.617 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.616 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.616 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.616 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.612 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.608 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.607 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.606 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.604 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.601 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.598 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.596 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.594 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.594 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.593 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.593 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.593 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.592 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.592 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.591 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.591 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.590 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.589 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.585 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.584 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.584 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.583 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.579 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.571 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.569 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.566 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.564 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.562 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.560 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.560 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.560 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.555 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.552 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.546 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.542 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.530 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.515 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.514 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.509 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.502 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.502 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.499 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.499 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.496 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.492 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.491 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.490 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.486 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.483 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.480 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.479 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.475 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.475 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.474 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.472 | |
| 3eks | CY9 | Actin-5C | / | 0.471 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.466 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.465 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.465 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.463 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.463 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.463 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.463 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.463 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.462 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.462 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.462 | |
| 1c7o | PPG | Hemolysin | / | 0.461 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.461 | |
| 3eku | CY9 | Actin-5C | / | 0.461 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.460 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.460 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.458 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.458 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.457 | |
| 2xlt | NA0 | Putative flavin-containing monooxygenase | / | 0.457 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.457 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.457 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.457 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.456 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.456 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.456 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.456 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 4h6p | FMN | Chromate reductase | / | 0.455 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.455 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.451 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.450 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1fml | RTL | Retinol dehydratase | / | 0.449 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.449 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.447 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.447 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.447 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.447 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.446 | |
| 2uyw | BTN | Avd protein | / | 0.446 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.446 | |
| 2pca | SAH | Diphthine synthase | / | 0.445 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.445 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.445 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.445 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.444 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.444 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.444 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.444 | |
| 4gdc | NDP | UDP-galactopyranose mutase | / | 0.444 | |
| 1d0m | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.443 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.443 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.442 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.441 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.440 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.440 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 |