Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T82739 | Target Info | |||
| Target Name | Plasma kallikrein (KLKB1) | ||||
| Synonyms | Plasma prekallikrein; Plasma kallikrein light chain; Plasma kallikrein heavy chain; PKK; Kininogenin; KLK3; Fletcher factor | ||||
| Target Type | Successful Target | ||||
| Gene Name | KLKB1 | ||||
| Biochemical Class | Peptidase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Glutathione | Ligand Info | |||||
| Structure Description | human plasmakallikrein protease domain in complex with active site directed inhibitor | PDB:6T7P | ||||
| Method | X-ray diffraction | Resolution | 1.42 Å | Mutation | No | [1] |
| PDB Sequence |
IVGGTNSSWG
25 EWPWQVSLQV35 KLTAQRHLCG43 GSLIGHQWVL53 TAAHCFDGLP60C LQDVWRIYSG 69 ILNLSDITKD79 TPFSQIKEII89 IHQNYKVSEG99 NHDIALIKLQ109 APLNYTEFQK 119 PICLPSKGDT129 STIYTNCWVT139 GWGFSKEKGE150 IQNILQKVNI160 PLVTNEECQK 170 RYQDYKITQR179 MVCAGYKEGG187A KDACKGDSGG197 PLVCKHNGMW207 RLVGITSWGE 217 GCARREQPGV227 YTKVAEYMDW237 ILEKTQS
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| Ligand Name: Benzamidine | Ligand Info | |||||
| Structure Description | Allosteric activation of human prekallikrein by apple domain disc rotation | PDB:6I44 | ||||
| Method | X-ray diffraction | Resolution | 1.36 Å | Mutation | No | [2] |
| PDB Sequence |
GCLTQLYENA
10 FFRGGDVASM20 YTPNAQYCQM30 RCTFHPRCLL40 FSFLPASSIN50 DMEKRFGCFL 60 KDSVTGTLPK70 VHRTGAVSGH80 SLKQCGHQIS90 ACHRDIYKGV100 DMRGVNFNVS 110 KVSSVEECQK120 RCTNNIRCQF130 FSYATQTFHK140 AEYRNNCLLK150 YSPGGTPTAI 160 KVLSNVESGF170 SLKPCALSEI180 GCHMNIFQHL190 AFSDVDVARV200 LTPDAFVCRT 210 ICTYHPNCLF220 FTFYTNVWKI230 ESQRNVCLLK240 TSESGTPSSS250 TPQENTISGY 260 SLLTCKRTLP270 EPCHSKIYPG280 VDFGGEELNV290 TFVKGVNVCQ300 ETCTKMIRCQ 310 FFTYSLLPED320 CKAEACKCFL330 RLSMDGSPTR340 IAYGTQGSSG350 YSLRLCNTVC 364 TIVGGTQSSW380 GEWPWQVSLQ390 VKLTAQRHLC400 GGSLIGHQWV410 LTAAHCFDGL 420 PLQDVWRIYS430 GILQLSDITK440 DTPFSQIKEI450 IIHQNYKVSE460 GNHDIALIKL 470 QAPLQYTEFQ480 KPICLPSIYT496 NCWVTGWGFS506 AEAGEIQNIL516 QKVNIPLVTN 526 EECQKRYQDY536 KITQRMVCAG546 YKEGGKDACK556 GDAGGPLVCK566 HNGMWRLVGI 576 TSWGEGCARR586 EQPGVYTKVA596 EYMDWILEKT606 QSSD
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: L-serine | Ligand Info | |||||
| Structure Description | Allosteric activation of human prekallikrein by apple domain disc rotation | PDB:6I44 | ||||
| Method | X-ray diffraction | Resolution | 1.36 Å | Mutation | No | [2] |
| PDB Sequence |
GCLTQLYENA
10 FFRGGDVASM20 YTPNAQYCQM30 RCTFHPRCLL40 FSFLPASSIN50 DMEKRFGCFL 60 KDSVTGTLPK70 VHRTGAVSGH80 SLKQCGHQIS90 ACHRDIYKGV100 DMRGVNFNVS 110 KVSSVEECQK120 RCTNNIRCQF130 FSYATQTFHK140 AEYRNNCLLK150 YSPGGTPTAI 160 KVLSNVESGF170 SLKPCALSEI180 GCHMNIFQHL190 AFSDVDVARV200 LTPDAFVCRT 210 ICTYHPNCLF220 FTFYTNVWKI230 ESQRNVCLLK240 TSESGTPSSS250 TPQENTISGY 260 SLLTCKRTLP270 EPCHSKIYPG280 VDFGGEELNV290 TFVKGVNVCQ300 ETCTKMIRCQ 310 FFTYSLLPED320 CKAEACKCFL330 RLSMDGSPTR340 IAYGTQGSSG350 YSLRLCNTVC 364 TIVGGTQSSW380 GEWPWQVSLQ390 VKLTAQRHLC400 GGSLIGHQWV410 LTAAHCFDGL 420 PLQDVWRIYS430 GILQLSDITK440 DTPFSQIKEI450 IIHQNYKVSE460 GNHDIALIKL 470 QAPLQYTEFQ480 KPICLPSIYT496 NCWVTGWGFS506 AEAGEIQNIL516 QKVNIPLVTN 526 EECQKRYQDY536 KITQRMVCAG546 YKEGGKDACK556 GDAGGPLVCK566 HNGMWRLVGI 576 TSWGEGCARR586 EQPGVYTKVA596 EYMDWILEKT606 QSSD
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SER or .SER2 or .SER3 or :3SER;style chemicals stick;color identity;select .A:184 or .A:205 or .A:206 or .A:207 or .A:209 or .A:210 or .A:213 or .A:262 or .A:270; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Piperidine-1-carboxamidine | Ligand Info | |||||
| Structure Description | The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor pkalin-1 | PDB:5F8Z | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | Yes | [3] |
| PDB Sequence |
IVGGTNSSWG
25 EWPWQVSLQV35 KLTAQRHLCG43 GSLIGHQWVL53 TAAHCFDGLP60C LQDVWRIYSG 69 ILNLSDITKD79 TPFSQIKEII89 IHQNYKVSEG99 NHDIALIKLQ109 APLNYTEFQK 119 PISLPSKGDT129 STIYTNCWVT139 GWGFSKEKGE150 IQNILQKVNI160 PLVTNEECQK 170 RYQDYKITQR179 MVCAGYKEGG186B KDACKGDSGG197 PLVCKHNGMW208C RLVGITSWGE 217 GCARREQPGV227 YTKVAEYMDW237 ILEKTQSSD
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MRZ or .MRZ2 or .MRZ3 or :3MRZ;style chemicals stick;color identity;select .A:189 or .A:190 or .A:191 or .A:192 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:219 or .A:220 or .A:221 or .A:226 or .A:227 or .A:228; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (8e)-3-Amino-1-Methyl-15-[(1h-Pyrazol-1-Yl)methyl]-7,10,11,12,24,25-Hexahydro-6h,18h,23h-19,22-(Metheno)pyrido[4,3-J][1,9,13,17,18]benzodioxatriazacyclohenicosin-23-One | Ligand Info | |||||
| Structure Description | Structure of human plasma kallikrein | PDB:5TJX | ||||
| Method | X-ray diffraction | Resolution | 1.41 Å | Mutation | Yes | [4] |
| PDB Sequence |
IVGGTESSWG
400 EWPWQVSLQV410 KLTAQRHLCG420 GSLIGHQWVL430 TAAHCFDGLP440 LQDVWRIYSG 450 ILELSDITKD460 TPFSQIKEII470 IHQNYKVSEG480 NHDIALIKLQ490 APLEYTEFQK 500 PISLPSTIYT515 NCWVTGWGFS525 KEKGEIQNIL535 QKVNIPLVTN545 EECQKRYQDY 555 KITQRMVCAG565 YKEGGKDACK575 GDSGGPLVCK585 HNGMWRLVGI595 TSWGEGCARR 605 EQPGVYTKVA615 EYMDWILEKT625 Q
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GBT or .GBT2 or .GBT3 or :3GBT;style chemicals stick;color identity;select .A:434 or .A:437 or .A:475 or .A:478 or .A:479 or .A:480 or .A:481 or .A:483 or .A:555 or .A:556 or .A:557 or .A:561 or .A:572 or .A:573 or .A:574 or .A:575 or .A:576 or .A:577 or .A:578 or .A:596 or .A:597 or .A:598 or .A:599 or .A:600 or .A:601 or .A:602 or .A:603 or .A:610; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS434
3.355
ASP437
4.382
TYR475
4.119
SER478
2.632
GLU479
3.038
GLY480
3.192
ASN481
4.092
ASP483
2.916
TYR555
2.747
LYS556
3.357
ILE557
2.970
MET561
3.180
ASP572
2.571
ALA573
2.639
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| Ligand Name: N-[(6-Amino-2,4-Dimethylpyridin-3-Yl)methyl]-1-({4-[(1h-Pyrazol-1-Yl)methyl]phenyl}methyl)-1h-Pyrazole-4-Carboxamide | Ligand Info | |||||
| Structure Description | Structure of human plasma kallikrein protease domain with inhibitor | PDB:6O1S | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [5] |
| PDB Sequence |
IVGGTESSWG
400 EWPWQVSLQV410 KLTAQRHLCG420 GSLIGHQWVL430 TAAHCFDGLP440 LQDVWRIYSG 450 ILELSDITKD460 TPFSQIKEII470 IHQNYKVSEG480 NHDIALIKLQ490 APLEYTEFQK 500 PISLPSKGDT510 STIYTNCWVT520 GWGFSKEKGE530 IQNILQKVNI540 PLVTNEECQK 550 RYQDYKITQR560 MVCAGYKEGG570 KDACKGDSGG580 PLVCKHNGMW590 RLVGITSWGE 600 GCARREQPGV610 YTKVAEYMDW620 ILEKTQSSD
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7SD or .7SD2 or .7SD3 or :37SD;style chemicals stick;color identity;select .E:434 or .E:475 or .E:478 or .E:479 or .E:480 or .E:481 or .E:483 or .E:555 or .E:556 or .E:557 or .E:561 or .E:572 or .E:573 or .E:574 or .E:575 or .E:576 or .E:577 or .E:578 or .E:596 or .E:597 or .E:598 or .E:599 or .E:600 or .E:601 or .E:602 or .E:603 or .E:609 or .E:610; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS434
3.130
TYR475
4.421
SER478
3.285
GLU479
3.299
GLY480
3.495
ASN481
3.915
ASP483
2.778
TYR555
2.710
LYS556
3.245
ILE557
3.068
MET561
3.152
ASP572
2.533
ALA573
3.146
CYS574
2.651
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (2~{S},4~{R})-1-[[(3~{S})-3-azanyl-2,3-dihydro-1-benzofuran-6-yl]carbonyl]-~{N}-(3-chlorophenyl)-4-phenyl-pyrrolidine-2-carboxamide | Ligand Info | |||||
| Structure Description | human plasmakallikrein protease domain in complex with active site directed inhibitor | PDB:6T7P | ||||
| Method | X-ray diffraction | Resolution | 1.42 Å | Mutation | No | [1] |
| PDB Sequence |
IVGGTNSSWG
25 EWPWQVSLQV35 KLTAQRHLCG43 GSLIGHQWVL53 TAAHCFDGLP60C LQDVWRIYSG 69 ILNLSDITKD79 TPFSQIKEII89 IHQNYKVSEG99 NHDIALIKLQ109 APLNYTEFQK 119 PICLPSKGDT129 STIYTNCWVT139 GWGFSKEKGE150 IQNILQKVNI160 PLVTNEECQK 170 RYQDYKITQR179 MVCAGYKEGG187A KDACKGDSGG197 PLVCKHNGMW207 RLVGITSWGE 217 GCARREQPGV227 YTKVAEYMDW237 ILEKTQS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MU8 or .MU82 or .MU83 or :3MU8;style chemicals stick;color identity;select .A:39 or .A:40 or .A:41 or .A:57 or .A:102 or .A:143 or .A:151 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:219 or .A:220 or .A:221 or .A:226 or .A:227 or .A:228; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ARG39
3.864
HIS40
2.882
LEU41
3.601
HIS57
3.282
ASP102
4.762
PHE143
4.180
ILE151
3.761
ASP189
2.800
ALA190
2.813
CYS191
3.317
LYS192
3.132
GLY193
3.069
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structure-Based Design and Preclinical Characterization of Selective and Orally Bioavailable Factor XIa Inhibitors: Demonstrating the Power of an Integrated S1 Protease Family Approach. J Med Chem. 2020 Aug 13;63(15):8088-8113. | ||||
| REF 2 | Plasma kallikrein structure reveals apple domain disc rotated conformation compared to factor XI. J Thromb Haemost. 2019 May;17(5):759-770. | ||||
| REF 3 | The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor pkalin-1 | ||||
| REF 4 | Structure-Guided Design of Novel, Potent, and Selective Macrocyclic Plasma Kallikrein Inhibitors. ACS Med Chem Lett. 2016 Dec 6;8(2):185-190. | ||||
| REF 5 | Structures of full-length plasma kallikrein bound to highly specific inhibitors describe a new mode of targeted inhibition. J Struct Biol. 2019 May 1;206(2):170-182. | ||||
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