Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T02392 Target Info
Target Name HUMAN dipeptidyl peptidase 1 (CTSC)
Synonyms Dipeptidyl transferase; Dipeptidyl peptidase 1; DPPI; DPP-I; Cysteine protease dipeptidyl peptidase I; Cathepsin J; Cathepsin C; CPPI
Gene Name CTSC
Biochemical Class Peptidase
UniProt ID
CATC_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: L-tyrosine Ligand Info
Structure Description Crystal structure of Cathepsin C in complex with dipeptide substrates PDB:4OEL
Method X-ray diffraction Resolution 1.40 Å Mutation Yes [1]
PDB Sequence
> Chain A
DTPANCTYLD
10
LLGTWVFQVG
20
SSGSQRDVNC
30
SVMGPQEKKV
40
VVYLQKLDTA
50

YDDLGNSGHF
60
TIIYNQGFEI
70
VLNDYKWFAF
80
FKYKEEGSKV
90
TTYCNETMTG
100

WVHDVLGRNW
110
ACFTGKKVLH
206
LPTSWDWRNV
216
HGINFVSPVR
226
NQASCGSCYS
236

FASMGMLEAR
246
IRILTNNSQT
256
PILSPQEVVS
266
CSQYAQGCEG
276
GFPYLIAGKY
286

AQDFGLVEEA
296
CFPYTGTDSP
306
CKMKEDCFRY
316
YSSEYHYVGG
326
FYGGCNEALM
336

KLELVHHGPM
346
AVAFEVYDDF
356
LHYKKGIYHH
366
T
> Chain B
PFNPFELTNH
381
AVLLVGYGTD
391
SASGMDYWIV
401
KNSWGTGWGE
411
NGYFRIRRGT
421

DECAIESIAV
431
AATPIPKLE
Residue
Distance (Å)
ASP1[A]
3.564
GLN228[A]
3.008
CYS231[A]
4.517
GLY232[A]
3.455
SER233[A]
3.679
CYS234[A]
1.784
TYR235[A]
4.461
Residue
Distance (Å)
CYS274[A]
4.772
GLU275[A]
3.202
GLY276[A]
3.872
ASN380[B]
2.893
HIS381[B]
3.940
ALA382[B]
4.772
Ligand Name: L-serine Ligand Info
Structure Description Crystal structure of Cathepsin C in complex with dipeptide substrates PDB:4OEL
Method X-ray diffraction Resolution 1.40 Å Mutation Yes [1]
PDB Sequence
> Chain A
DTPANCTYLD
10
LLGTWVFQVG
20
SSGSQRDVNC
30
SVMGPQEKKV
40
VVYLQKLDTA
50

YDDLGNSGHF
60
TIIYNQGFEI
70
VLNDYKWFAF
80
FKYKEEGSKV
90
TTYCNETMTG
100

WVHDVLGRNW
110
ACFTGKKVLH
206
LPTSWDWRNV
216
HGINFVSPVR
226
NQASCGSCYS
236

FASMGMLEAR
246
IRILTNNSQT
256
PILSPQEVVS
266
CSQYAQGCEG
276
GFPYLIAGKY
286

AQDFGLVEEA
296
CFPYTGTDSP
306
CKMKEDCFRY
316
YSSEYHYVGG
326
FYGGCNEALM
336

KLELVHHGPM
346
AVAFEVYDDF
356
LHYKKGIYHH
366
T
> Chain B
PFNPFELTNH
381
AVLLVGYGTD
391
SASGMDYWIV
401
KNSWGTGWGE
411
NGYFRIRRGT
421

DECAIESIAV
431
AATPIPKLE
Residue
Distance (Å)
ASP1[A]
2.773
GLY232[A]
4.212
CYS234[A]
3.467
TYR235[A]
3.682
GLY276[A]
3.158
GLY277[A]
2.805
Residue
Distance (Å)
PHE278[A]
3.306
PRO279[A]
4.067
ALA349[A]
4.622
ASN380[B]
3.753
HIS381[B]
3.837
ALA382[B]
3.335
Ligand Name: L-lysine Ligand Info
Structure Description Crystal structure of Cathepsin C in complex with dipeptide substrates PDB:4OEM
Method X-ray diffraction Resolution 1.52 Å Mutation Yes [1]
PDB Sequence
> Chain A
DTPANCTYLD
10
LLGTWVFQVG
20
SSGSQRDVNC
30
SVMGPQEKKV
40
VVYLQKLDTA
50

YDDLGNSGHF
60
TIIYNQGFEI
70
VLNDYKWFAF
80
FKYKEEGSKV
90
TTYCNETMTG
100

WVHDVLGRNW
110
ACFTGKKVHL
207
PTSWDWRNVH
217
GINFVSPVRN
227
QASCGSCYSF
237

ASMGMLEARI
247
RILTNNSQTP
257
ILSPQEVVSC
267
SQYAQGCEGG
277
FPYLIAGKYA
287

QDFGLVEEAC
297
FPYTGTDSPC
307
KMKEDCFRYY
317
SSEYHYVGGF
327
YGGCNEALMK
337

LELVHHGPMA
347
VAFEVYDDFL
357
HYKKGIYHHT
367

> Chain B
FNPFELTNHA
382
VLLVGYGTDS
392
ASGMDYWIVK
402
NSWGTGWGEN
412
GYFRIRRGTD
422

ECAIESIAVA
432
ATPIPKLE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LYS or .LYS2 or .LYS3 or :3LYS;style chemicals stick;color identity;select .A:1 or .A:228 or .A:231 or .A:232 or .A:233 or .A:234 or .A:235 or .A:274 or .A:275 or .A:276 or .A:277 or .B:380 or .B:381 or .B:382; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASP1[A]
3.131
GLN228[A]
2.028
CYS231[A]
4.576
GLY232[A]
2.768
SER233[A]
3.811
CYS234[A]
1.819
TYR235[A]
3.829
Residue
Distance (Å)
CYS274[A]
4.861
GLU275[A]
3.324
GLY276[A]
3.305
GLY277[A]
4.357
ASN380[B]
3.103
HIS381[B]
3.064
ALA382[B]
3.935
Ligand Name: Gly-Phe-DMK Ligand Info
Structure Description Crystal Structure of human dipeptidyl peptidase I (Cathepsin C) in complex with the inhibitor Gly-Phe-CHN2 PDB:2DJF
Method X-ray diffraction Resolution 2.00 Å Mutation No [2]
PDB Sequence
> Chain A
DTPANCTYLD
10
LLGTWVFQVG
20
SSGSQRDVNC
30
SVMGPQEKKV
40
VVYLQKLDTA
50

YDDLGNSGHF
60
TIIYNQGFEI
70
VLNDYKWFAF
80
FKYKEEGSKV
90
TTYCNETMTG
100

WVHDVLGRNW
110
ACFTGKKV
> Chain B
LPTSWDWRNV
216
HGINFVSPVR
226
NQASCGSCYS
236
FASMGMLEAR
246
IRILTNNSQT
256

PILSPQEVVS
266
CSQYAQGCEG
276
GFPYLIAGKY
286
AQDFGLVEEA
296
CFPYTGTDSP
306

CKMKEDCFRY
316
YSSEYHYVGG
326
FYGGCNEALM
336
KLELVHHGPM
346
AVAFEVYDDF
356

LHYKKGIYHH
366
T
> Chain C
PFNPFELTNH
381
AVLLVGYGTD
391
SASGMDYWIV
401
KNSWGTGWGE
411
NGYFRIRRGT
421

DECAIESIAV
431
AATPIPKL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1ZB or .1ZB2 or .1ZB3 or :31ZB;style chemicals stick;color identity;select .A:1 or .B:228 or .B:231 or .B:232 or .B:233 or .B:234 or .B:235 or .B:274 or .B:275 or .B:276 or .B:277 or .B:278 or .C:380 or .C:381 or .C:382; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASP1[A]
2.817
GLN228[B]
3.028
CYS231[B]
4.224
GLY232[B]
2.953
SER233[B]
3.141
CYS234[B]
1.860
TYR235[B]
3.733
CYS274[B]
4.392
Residue
Distance (Å)
GLU275[B]
3.130
GLY276[B]
3.097
GLY277[B]
3.006
PHE278[B]
3.238
ASN380[C]
3.139
HIS381[C]
3.209
ALA382[C]
4.162
Ligand Name: 2,5-dibromo-N-{(3R,5S)-1-[(Z)-iminomethyl]-5-methylpyrrolidin-3-yl}benzenesulfonamide Ligand Info
Structure Description Discovery of Novel Cyanamide-Based Inhibitors of Cathepsin C PDB:3PDF
Method X-ray diffraction Resolution 1.85 Å Mutation No [3]
PDB Sequence
DTPANCTYLD
10
LLGTWVFQVG
20
SSGSQRDVNC
30
SVMGPQEKKV
40
VVYLQKLDTA
50

YDDLGNSGHF
60
TIIYNQGFEI
70
VLNDYKWFAF
80
FKYKEEGSKV
90
TTYCNETMTG
100

WVHDVLGRNW
110
ACFTGKKVFL
207
PTSWDWRNVH
217
GINFVSPVRN
227
QASCGSCYSF
237

ASMGMLEARI
247
RILTNNSQTP
257
ILSPQEVVSC
267
SQYAQGCEGG
277
FPYLIAGKYA
287

QDFGLVEEAC
297
FPYTGTDSPC
307
KMKEDCFRYY
317
SSEYHYVGGF
327
YGGCNEALMK
337

LELVHHGPMA
347
VAFEVYDDFL
357
HYKKGIYHHT
367
DPFNPFELTN
380
HAVLLVGYGT
390

DSASGMDYWI
400
VKNSWGTGWG
410
ENGYFRIRRG
420
TDECAIESIA
430
VAATPIPKLE
440

N
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LXV or .LXV2 or .LXV3 or :3LXV;style chemicals stick;color identity;select .A:1 or .A:64 or .A:228 or .A:231 or .A:232 or .A:233 or .A:234 or .A:235 or .A:274 or .A:275 or .A:276 or .A:277 or .A:278 or .A:279 or .A:349 or .A:379 or .A:380 or .A:381 or .A:382 or .A:429; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASP1
2.965
TYR64
3.638
GLN228
3.056
CYS231
4.752
GLY232
3.575
SER233
3.713
CYS234
1.625
TYR235
4.088
CYS274
4.747
GLU275
4.315
Residue
Distance (Å)
GLY276
3.215
GLY277
2.896
PHE278
3.246
PRO279
3.563
ALA349
3.700
THR379
3.136
ASN380
3.237
HIS381
4.109
ALA382
3.884
ILE429
4.757
Ligand Name: (2S,4S)-N-[(2S)-1-azanylidene-3-[4-(4-cyanophenyl)phenyl]propan-2-yl]-4-oxidanyl-piperidine-2-carboxamide Ligand Info
Structure Description Human DPP1 in complex with (2S,4S)-N-((1S)-1-cyano-2-(4-(4- cyanophenyl)phenyl)ethyl)-4-hydroxy-piperidine-2-carboxamide PDB:4CDF
Method X-ray diffraction Resolution 2.20 Å Mutation No [4]
PDB Sequence
> Chain A
DTPANCTYLD
10
LLGTWVFQVG
20
SSGSQRDVNC
30
SVMGPQEKKV
40
VVYLQKLDTA
50

YDDLGNSGHF
60
TIIYNQGFEI
70
VLNDYKWFAF
80
FKYKEEGSKV
90
TTYCNETMTG
100

WVHDVLGRNW
110
ACFTGKKVGT
120

> Chain B
HLPTSWDWRN
215
VHGINFVSPV
225
RNQASCGSCY
235
SFASMGMLEA
245
RIRILTNNSQ
255

TPILSPQEVV
265
SCSQYAQGCE
275
GGFPYLIAGK
285
YAQDFGLVEE
295
ACFPYTGTDS
305

PCKMKEDCFR
315
YYSSEYHYVG
325
GFYGGCNEAL
335
MKLELVHHGP
345
MAVAFEVYDD
355

FLHYKKGIYH
365
HT
> Chain C
PFNPFELTNH
381
AVLLVGYGTD
391
SASGMDYWIV
401
KNSWGTGWGE
411
NGYFRIRRGT
421

DECAIESIAV
431
AATPIPKL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .W2C or .W2C2 or .W2C3 or :3W2C;style chemicals stick;color identity;select .A:1 or .A:2 or .A:3 or .A:64 or .B:228 or .B:231 or .B:232 or .B:233 or .B:234 or .B:235 or .B:274 or .B:275 or .B:276 or .B:277 or .B:278 or .B:349 or .C:379 or .C:380 or .C:381 or .C:382; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASP1[A]
2.843
THR2[A]
3.759
PRO3[A]
3.248
TYR64[A]
4.657
GLN228[B]
3.018
CYS231[B]
4.536
GLY232[B]
3.605
SER233[B]
3.819
CYS234[B]
1.769
TYR235[B]
3.713
Residue
Distance (Å)
CYS274[B]
4.636
GLU275[B]
3.602
GLY276[B]
3.194
GLY277[B]
2.924
PHE278[B]
3.524
ALA349[B]
3.991
THR379[C]
2.635
ASN380[C]
2.846
HIS381[C]
3.747
ALA382[C]
4.085
Ligand Name: (2S)-N-[(2S)-1-AZANYLIDENE-3-[4-(4-CYANOPHENYL)PHENYL]PROPAN-2-YL]PIPERIDINE-2-CARBOXAMIDE Ligand Info
Structure Description Human DPP1 in complex with (2S)-N-((1S)-1-cyano-2-(4-(4-cyanophenyl) phenyl)ethyl)piperidine-2-carboxamide PDB:4CDD
Method X-ray diffraction Resolution 2.35 Å Mutation No [4]
PDB Sequence
> Chain A
DTPANCTYLD
10
LLGTWVFQVG
20
SSGSQRDVNC
30
SVMGPQEKKV
40
VVYLQKLDTA
50

YDDLGNSGHF
60
TIIYNQGFEI
70
VLNDYKWFAF
80
FKYKEEGSKV
90
TTYCNETMTG
100

WVHDVLGRNW
110
ACFTGKKV
> Chain B
HLPTSWDWRN
215
VHGINFVSPV
225
RNQASCGSCY
235
SFASMGMLEA
245
RIRILTNNSQ
255

TPILSPQEVV
265
SCSQYAQGCE
275
GGFPYLIAGK
285
YAQDFGLVEE
295
ACFPYTGTDS
305

PCKMKEDCFR
315
YYSSEYHYVG
325
GFYGGCNEAL
335
MKLELVHHGP
345
MAVAFEVYDD
355

FLHYKKGIYH
365
HT
> Chain C
PFNPFELTNH
381
AVLLVGYGTD
391
SASGMDYWIV
401
KNSWGTGWGE
411
NGYFRIRRGT
421

DECAIESIAV
431
AATPIPKL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GDI or .GDI2 or .GDI3 or :3GDI;style chemicals stick;color identity;select .A:1 or .A:2 or .A:3 or .A:64 or .B:228 or .B:231 or .B:232 or .B:233 or .B:234 or .B:235 or .B:274 or .B:275 or .B:276 or .B:277 or .B:278 or .B:349 or .C:379 or .C:380 or .C:381 or .C:382; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASP1[A]
2.641
THR2[A]
3.737
PRO3[A]
3.266
TYR64[A]
4.486
GLN228[B]
3.196
CYS231[B]
4.707
GLY232[B]
3.699
SER233[B]
3.926
CYS234[B]
1.785
TYR235[B]
3.973
Residue
Distance (Å)
CYS274[B]
4.501
GLU275[B]
3.327
GLY276[B]
3.189
GLY277[B]
3.037
PHE278[B]
3.417
ALA349[B]
3.739
THR379[C]
3.674
ASN380[C]
2.660
HIS381[C]
3.916
ALA382[C]
3.910
Ligand Name: (2S)-2-azanyl-N-[(2S)-1-azanylidene-3-(4-phenylphenyl)propan-2-yl]butanamide Ligand Info
Structure Description Human DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4- phenylphenyl)ethyl)butanamide PDB:4CDC
Method X-ray diffraction Resolution 2.40 Å Mutation No [4]
PDB Sequence
> Chain A
DTPANCTYLD
10
LLGTWVFQVG
20
SSGSQRDVNC
30
SVMGPQEKKV
40
VVYLQKLDTA
50

YDDLGNSGHF
60
TIIYNQGFEI
70
VLNDYKWFAF
80
FKYKVTTYCN
95
ETMTGWVHDV
105

LGRNWACFTG
115
KKVG
> Chain B
HLPTSWDWRN
215
VHGINFVSPV
225
RNQASCGSCY
235
SFASMGMLEA
245
RIRILTNNSQ
255

TPILSPQEVV
265
SCSQYAQGCE
275
GGFPYLIAGK
285
YAQDFGLVEE
295
ACFPYTGTDS
305

PCKMKEDCFR
315
YYSSEYHYVG
325
GFYGGCNEAL
335
MKLELVHHGP
345
MAVAFEVYDD
355

FLHYKKGIYH
365
HT
> Chain C
PFNPFELTNH
381
AVLLVGYGTD
391
SASGMDYWIV
401
KNSWGTGWGE
411
NGYFRIRRGT
421

DECAIESIAV
431
AATPIPKL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6AO or .6AO2 or .6AO3 or :36AO;style chemicals stick;color identity;select .A:1 or .A:2 or .A:3 or .B:228 or .B:231 or .B:232 or .B:233 or .B:234 or .B:235 or .B:275 or .B:276 or .B:277 or .B:278 or .B:279 or .B:349 or .C:379 or .C:380 or .C:381 or .C:382; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASP1[A]
2.588
THR2[A]
3.922
PRO3[A]
4.663
GLN228[B]
3.374
CYS231[B]
4.921
GLY232[B]
3.865
SER233[B]
4.195
CYS234[B]
1.793
TYR235[B]
3.924
GLU275[B]
3.516
Residue
Distance (Å)
GLY276[B]
3.190
GLY277[B]
2.851
PHE278[B]
3.279
PRO279[B]
4.784
ALA349[B]
3.875
THR379[C]
3.901
ASN380[C]
2.723
HIS381[C]
3.903
ALA382[C]
3.977
Ligand Name: 4-AZANYL-N-[(2S)-1-AZANYLIDENE-3-[4-(4-CYANOPHENYL)PHENYL]PROPAN-2-YL]OXANE-4-CARBOXAMIDE Ligand Info
Structure Description Human DPP1 in complex with 4-amino-N-((1S)-1-cyano-2-(4-(4- cyanophenyl)phenyl)ethyl)tetrahydropyran-4-carboxamide PDB:4CDE
Method X-ray diffraction Resolution 2.40 Å Mutation No [4]
PDB Sequence
> Chain A
DTPANCTYLD
10
LLGTWVFQVG
20
SSGSQRDVNC
30
SVMGPQEKKV
40
VVYLQKLDTA
50

YDDLGNSGHF
60
TIIYNQGFEI
70
VLNDYKWFAF
80
FKYKEEGSKV
90
TTYCNETMTG
100

WVHDVLGRNW
110
ACFTGKKV
> Chain B
HLPTSWDWRN
215
VHGINFVSPV
225
RNQASCGSCY
235
SFASMGMLEA
245
RIRILTNNSQ
255

TPILSPQEVV
265
SCSQYAQGCE
275
GGFPYLIAGK
285
YAQDFGLVEE
295
ACFPYTGTDS
305

PCKMKEDCFR
315
YYSSEYHYVG
325
GFYGGCNEAL
335
MKLELVHHGP
345
MAVAFEVYDD
355

FLHYKKGIYH
365
H
> Chain C
PFNPFELTNH
381
AVLLVGYGTD
391
SASGMDYWIV
401
KNSWGTGWGE
411
NGYFRIRRGT
421

DECAIESIAV
431
AATPIPKL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .U6B or .U6B2 or .U6B3 or :3U6B;style chemicals stick;color identity;select .A:1 or .A:2 or .A:3 or .A:64 or .B:228 or .B:232 or .B:233 or .B:234 or .B:235 or .B:275 or .B:276 or .B:277 or .B:278 or .B:349 or .C:379 or .C:380 or .C:381 or .C:382; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASP1[A]
2.939
THR2[A]
4.032
PRO3[A]
3.481
TYR64[A]
4.239
GLN228[B]
3.397
GLY232[B]
3.748
SER233[B]
4.545
CYS234[B]
1.771
TYR235[B]
3.636
Residue
Distance (Å)
GLU275[B]
3.408
GLY276[B]
3.079
GLY277[B]
2.663
PHE278[B]
3.485
ALA349[B]
3.982
THR379[C]
2.858
ASN380[C]
2.919
HIS381[C]
3.415
ALA382[C]
3.806
References  Top
REF 1 The amino-acid substituents of dipeptide substrates of cathepsin C can determine the rate-limiting steps of catalysis. Biochemistry. 2012 Sep 25;51(38):7551-68.
REF 2 The crystal structure of human dipeptidyl peptidase I (cathepsin C) in complex with the inhibitor Gly-Phe-CHN2. Biochem J. 2007 Feb 1;401(3):645-50.
REF 3 Discovery of Novel Cyanamide-Based Inhibitors of Cathepsin C
REF 4 Cathepsin C inhibitors: property optimization and identification of a clinical candidate. J Med Chem. 2014 Mar 27;57(6):2357-67.

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