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 |
|---|---|---|---|
| 2v3h | I25 | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 1.000 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.711 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.699 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.699 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.695 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.689 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.688 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.686 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.684 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.679 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.670 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.668 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.667 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.658 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.657 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.654 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.654 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.650 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.650 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.643 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.642 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.640 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.639 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.637 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.637 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.636 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.633 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.631 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.629 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.629 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.627 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.626 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.626 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.622 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.622 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.621 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.620 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.618 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.618 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.618 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.616 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.615 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.613 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.613 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.612 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.611 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.611 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.610 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.610 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.610 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.609 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.608 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.605 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.605 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.605 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.604 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.604 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.603 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.602 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.601 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.601 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.600 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.596 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.595 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.594 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.594 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.593 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.593 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.592 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.590 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.589 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.587 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.586 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.586 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.584 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.584 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.583 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.580 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.579 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.578 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.578 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.577 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.570 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.570 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.570 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.567 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.559 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.555 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.553 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.552 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.550 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.549 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.549 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.549 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.546 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.546 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.544 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.542 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.540 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.539 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.536 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.535 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.532 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.529 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.529 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.516 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.511 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.510 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.509 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.504 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.503 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.496 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.496 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.487 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.487 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.486 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.480 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.479 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.478 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.476 | |
| 2nr4 | FMN | Conserved protein | / | 0.474 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.473 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.471 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.470 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.462 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.462 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.461 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.461 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.461 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.460 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.459 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.458 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.457 | |
| 1o1t | 2NH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.456 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.456 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.455 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.455 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.453 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.452 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.452 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.451 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.451 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.450 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.450 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.448 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.448 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.447 | |
| 2ptf | FMN | Uncharacterized protein MTH_863 | / | 0.447 | |
| 3eku | CY9 | Actin-5C | / | 0.447 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.447 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.446 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.446 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.446 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3ksq | Z96 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.445 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.445 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.444 | |
| 2ym1 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.444 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.443 | |
| 2c4f | GIL | Coagulation factor VII | 3.4.21.21 | 0.443 | |
| 2fa3 | ACO | Hydroxymethylglutaryl-CoA synthase | / | 0.443 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.443 | |
| 1fml | RTL | Retinol dehydratase | / | 0.442 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.442 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.442 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.442 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.442 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.442 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.441 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.441 | |
| 1ld7 | U66 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.440 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.440 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3ean | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.440 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.440 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.440 |