Receptor
PDB id Resolution Class Description Source Keywords
3VXE 1.25 Å EC: 3.4.21.5 HUMAN ALPHA-THROMBIN-BIVALIRUDIN COMPLEX AT PD5.0 HOMO SAPIENS SERINE PROTEASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: NEUTRON AND X-RAY CRYSTALLOGRAPHIC ANALYSIS OF THE ALPHA-THROMBIN-BIVALIRUDIN COMPLEX AT PD 5.0: PROTO STATES AND HYDRATION STRUCTURE OF THE ENZYME-PRODUC BIOCHIM.BIOPHYS.ACTA V.1834 1532 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DPN PRO ARG I:1;
 Valid;
 none;
 submit data
419.506 n/a O=C([...
NAG H:300;
 Invalid;
 none;
 submit data
221.208 C8 H15 N O6 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3VXE 1.25 Å EC: 3.4.21.5 HUMAN ALPHA-THROMBIN-BIVALIRUDIN COMPLEX AT PD5.0 HOMO SAPIENS SERINE PROTEASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: NEUTRON AND X-RAY CRYSTALLOGRAPHIC ANALYSIS OF THE ALPHA-THROMBIN-BIVALIRUDIN COMPLEX AT PD 5.0: PROTO STATES AND HYDRATION STRUCTURE OF THE ENZYME-PRODUC BIOCHIM.BIOPHYS.ACTA V.1834 1532 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 2HGT - DPN PRO ARG n/a n/a
2 3VXE - DPN PRO ARG n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 2HGT - DPN PRO ARG n/a n/a
2 3VXE - DPN PRO ARG n/a n/a
3 1TMT - DPN PRO ARG n/a n/a
50% Homology Family (115)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 4BAQ Ki = 0.98 nM M4Z C24 H36 N6 O3 [H]/N=C(/c....
2 2C8Z ic50 > 1 mM C2A C7 H8 Cl N c1cc(cc(c1....
3 1C1W - BAH C17 H18 N8 O2 c1cc2c(cc1....
4 4BAH Ki = 2.01 nM MEL C22 H31 N5 O4 c1cc(ccc1C....
5 2C90 ic50 = 330 uM C1M C7 H5 Cl N4 c1cc(ccc1n....
6 6ZUH ic50 = 27 nM N6H C22 H24 Cl N3 O4 CC1(CN(CCO....
7 3SHC Ki = 1.9 uM B01 C20 H23 Cl N4 O2 c1ccc(cc1)....
8 6T3Q Ki = 379 nM M6Q C20 H25 N5 O2 c1ccc(cc1)....
9 3SI3 Ki = 69.3 uM B03 C20 H24 N4 O2 c1ccc(cc1)....
10 4BAM Ki = 1.14 nM MM9 C24 H36 N6 O3 [H]/N=C(/c....
11 4YES Ki = 9.6 nM 45S C19 H23 Cl N4 O2 Cc1ccc([nH....
12 3DUX Ki = 100 nM 64U C21 H30 Cl N3 O2 c1cc(cc(c1....
13 1K22 Ki = 4 nM MEL C22 H31 N5 O4 c1cc(ccc1C....
14 2ZHQ Ki = 0.75 uM 27U C22 H26 N4 O2 [H]/N=C(/c....
15 3HAT - MBN ABN RNG GLY VAL ARG n/a n/a
16 2ZGX Ki = 180 nM 29U C17 H25 N5 O2 [H]/N=C(/c....
17 2ZC9 Ki = 180 nM 22U C21 H24 Cl N3 O2 c1ccc(cc1)....
18 3UTU Ki = 0.012 nM 1TS C32 H34 Cl N7 O6 S [H]/N=C(/c....
19 1G32 Ki = 780 nM R11 C25 H25 N7 [H]/N=C(/c....
20 3F68 Ki = 8.7 uM 91U C23 H32 Cl N3 O3 CC(=O)N[C@....
21 2ZFP Ki = 6.8 uM 19U C16 H22 Cl N3 O2 CC[C@H](C(....
22 1A4W Ki = 1.2 uM QWE C29 H40 N7 O4 S2 CN(C)c1ccc....
23 2ZGB Ki = 0.54 uM 21U C18 H26 Cl N3 O2 CC(C)C[C@H....
24 3SI4 Ki = 132.2 uM B04 C21 H27 N4 O2 C[n+]1cccc....
25 2C8X ic50 = 220 nM C5M C27 H33 Cl N2 O4 S Cc1cc(c(c(....
26 1C5O Ki = 320 uM BAM C7 H9 N2 c1ccc(cc1)....
27 2C8Y - C3M C20 H22 N2 O3 S c1ccc(cc1)....
28 1D4P Ka = 2000000 M^-1 BPP C22 H24 N4 O [H]/N=C(c1....
29 3SHA Ki = 2.6 uM P97 C20 H23 Cl N4 O2 c1ccc(cc1)....
30 6ZUU ic50 = 3900 nM QQN C22 H24 Cl N3 O4 C[C@@H]1CN....
31 2ZNK Ki = 0.02 uM 31U C19 H29 N5 O2 [H]/N=C(/c....
32 3QX5 Ki = 63.5 uM 02P C21 H26 Cl N4 O2 C[n+]1ccc(....
33 4BAK Ki = 1.22 nM M67 C25 H38 N6 O3 [H]/N=C(/c....
34 3P17 Ki = 33.4 uM 99P C20 H24 N4 O2 c1ccc(cc1)....
35 6ZUN ic50 = 10 nM QQ5 C22 H24 Cl N3 O4 C[C@@H]1CN....
36 1GHV Ki = 45 uM 120 C13 H12 N5 O c1cc2c(cc1....
37 1C1U - BAI C16 H14 N6 c1ccc2c(c1....
38 6ZV7 ic50 = 6 nM QQW C24 H28 Cl N3 O5 C[C@@H]1CN....
39 2ZI2 Ki = 5.7 uM 24U C17 H24 N4 O2 [H]/N=C(/c....
40 1QBV Ki = 4100 nM PPX C21 H27 N5 O2 c1ccc(cc1)....
41 3EGK Ki = 22 uM M18 C20 H27 Cl N2 O5 CC(C)(C)OC....
42 1D3P Ka = 24300000 M^-1 BT3 C32 H37 N3 O3 S c1cc(ccc1C....
43 1A2C ic50 = 0.5 uM 34H LEU PRJ OAR n/a n/a
44 6EO9 Ki = 160 nM 2OJ C40 H50 Cl N3 O14 S CC(C)N1CCC....
45 6ZUX ic50 = 4 nM QQE C24 H28 Cl N3 O5 C[C@H]1CN(....
46 3QTV Ki = 22.5 uM 06P C21 H27 N4 O2 C[n+]1ccc(....
47 1AIX - T19 C32 H34 B N3 O6 B([C@H](C(....
48 2ZDA - 32U C22 H28 N5 O2 c1ccc(cc1)....
49 1K21 Ki = 4.2 nM IGN C21 H38 N6 O4 C1CCC(CC1)....
50 4BAN Ki = 2.43 nM M6S C23 H34 N6 O3 [H]/N=C(/c....
51 6ROT Ki = 483.63 nM KDQ C22 H26 Cl N3 O5 S c1ccc(cc1)....
52 6T4A Ki = 140 nM J5K C20 H25 N5 O2 c1ccc(cc1)....
53 1G30 Ki = 140 nM T87 C29 H31 N7 O3 [H]/N=C(/c....
54 6EO8 Ki = 100 nM 2FN C32 H42 Cl N3 O10 S CC(C)N1CCC....
55 1MU6 Ki = 4.2 nM CDA C20 H19 F3 N6 O2 CC1=CN=C(C....
56 1FPC Ki = 0.1 uM 0ZI C25 H39 N6 O3 S NULL
57 6TDT Ki = 1213 nM LXW C26 H28 N4 O2 c1ccc(cc1)....
58 2ZF0 - 51U C22 H27 N3 O2 Cc1cccc(c1....
59 1W7G Ki ~ 13 uM MIU C20 H32 F3 N7 O3 S c1cc(cc(c1....
60 3DHK Ki = 47 nM 23U C27 H28 Cl N3 O2 c1ccc(cc1)....
61 2ZDV - 37U C21 H24 F N3 O2 c1ccc(cc1)....
62 2ZO3 Ki = 0.1 nM 33U C28 H31 N5 O2 [H]/N=C(/c....
63 1NRS - LEU ASP PRO ARG n/a n/a
64 3TU7 Ki = 8.17 nM 0BM C22 H34 N6 O4 S [H]/N=C(N)....
65 6GBW Ki = 3.51 nM EU5 C26 H36 Cl N7 O4 S [H]/N=C(N)....
66 6ZUW ic50 = 0.4 nM QQK C26 H32 Cl N3 O5 CC[C@@H]1C....
67 1KTS Ki = 4.5 nM C24 C27 H29 N7 O3 CCOC(=O)CC....
68 1GHY Ki = 0.008 uM 121 C13 H12 N5 O c1cc(c(nc1....
69 1MU8 Ki = 1 nM CDB C21 H23 F3 N6 O2 Cc1ccnc(c1....
70 1MUE Ki = 2.3 nM CDD C20 H17 Cl F3 N5 O3 c1ccc(c(c1....
71 2C8W ic50 = 3.7 nM C7M C25 H30 Cl N6 O4 S COc1ccc(cc....
72 1O5G Ki = 11 uM CR9 C21 H23 F N4 O2 C[C@H]1CCC....
73 1BCU Kd = 0.53 mM PRL C13 H11 N3 c1cc(cc2c1....
74 3QTO Ki = 74.8 uM 10P C21 H27 N4 O2 C[n+]1cccc....
75 1GHW Ki = 4 uM BMZ C14 H13 N4 O c1ccc(c(c1....
76 1C1V Ki = 0.023 uM BAB C17 H19 N8 c1cc2c(cc1....
77 1TOM Ki = 5 nM MIN C22 H34 N4 O2 CN[C@H](Cc....
78 1KTT ic50 = 1.5 uM C02 C22 H21 N5 O2 S Cn1c2ccc(c....
79 6ZV8 ic50 = 0.7 nM QQT C24 H27 Cl F N3 O5 C[C@H]1CN(....
80 3SV2 Ki = 64 uM P05 C20 H24 N4 O2 c1ccc(cc1)....
81 1O2G Ki = 0.76 uM 696 C21 H17 N3 O c1ccc(cc1)....
82 2C93 ic50 = 12 uM C4M C20 H28 N2 O4 S Cc1cc(c(c(....
83 4LXB ic50 = 7 nM 7R9 C26 H32 Cl F2 N5 O6 S2 CN(C)[C@H]....
84 3QWC Ki = 55.4 uM 98P C21 H26 Cl N4 O2 C[n+]1ccc(....
85 1D3D Ka = 1240000000 M^-1 BZT C32 H35 Br N2 O2 S c1cc(ccc1c....
86 4UFG - D6J C29 H35 N5 O4 S CC[C@@H](C....
87 5AFZ Kd = 0.16 uM UET C26 H29 N5 O4 S c1ccc(cc1)....
88 4UE7 Kd = 107 uM MRZ C6 H13 N3 [H]/N=C(N)....
89 3BIU - 10U C20 H29 N5 O2 c1cc(ccc1C....
90 4UFF - 6V2 C27 H31 N5 O4 S [H]/N=C(c1....
91 5AHG - Y4L C8 H11 Cl N2 O2 S CN(C)S(=O)....
92 3BIV - 11U C21 H31 N5 O2 [H]/N=C(/c....
93 4AX9 Ki = 0.00027 uM N5N C26 H34 N6 O6 S [H]/N=C(/N....
94 4UEH Kd = 355 uM BEN C7 H8 N2 [H]/N=C(c1....
95 4UFD - S49 C29 H33 N5 O4 S [H]/N=C(/c....
96 2V3O - I26 C24 H33 F N4 O3 [H]/N=C(/c....
97 5AF9 Kd = 1003 uM SJR C13 H12 N2 O2 COc1ccc(cc....
98 4UD9 Kd = 475 uM FQI C5 H4 Cl N O S c1cc(sc1C(....
99 1T4U - 81A C20 H25 N3 O7 S2 [H]/N=C(N)....
100 2R2M Ki = 47.1 nM I50 C19 H21 Cl F3 N5 O2 [H]/N=C(/N....
101 5AFY - WCE C7 H6 Cl N O c1cc(cc(c1....
102 6ZUG ic50 = 12 nM QPW C24 H28 Cl N3 O4 CCCN(C[C@@....
103 1T4V Ki = 0.021 uM 14A C19 H27 Cl N4 O3 C=CCN(C1CC....
104 4UFE - 3ZD C27 H31 N5 O4 S [H]/N=C(c1....
105 4UDW Kd = 0.27 uM N6L C21 H23 Cl2 N3 O2 c1ccc(cc1)....
106 2CF8 Ki = 0.008 uM ESH C26 H31 Cl N4 O [H]/N=C(c1....
107 2CF9 Ki = 0.015 uM 348 C27 H34 N4 O2 [H]/N=C(c1....
108 1VZQ Ki = 36 nM SHY C24 H24 N4 O5 [H]/N=C(c1....
109 2HGT - DPN PRO ARG n/a n/a
110 3VXE - DPN PRO ARG n/a n/a
111 1C4V Ki = 0.016 nM IH2 C30 H36 N6 O3 [H]/N=C(C1....
112 2V3H - I25 C24 H34 N4 O3 [H]/N=C(/c....
113 2CN0 Ki = 22 nM F25 C24 H27 F3 N4 O c1cc(ccc1C....
114 1OYT Ki = 0.057 uM FSN C23 H24 F N4 O2 c1cc(ccc1C....
115 1TMT - DPN PRO ARG n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DPN PRO ARG; Similar ligands found: 121
No: Ligand ECFP6 Tc MDL keys Tc
1 DPN PRO ARG 1 1
2 PHE PRO ARG 0.75 0.962963
3 DPN PRO DAR CYS NH2 0.734043 0.912281
4 DPN PRO DAR DTH NH2 0.729167 0.868852
5 DPN PRO DAR ILE NH2 0.71134 0.881356
6 THR LYS PRO ARG 0.608696 0.945455
7 PHE ASN ARG PRO VAL 0.590909 0.870968
8 HIS PRO PHE 0.561224 0.813559
9 TYR PRO PHE PHE NH2 0.54 0.741935
10 GLY PHE ARG PRO 0.539216 0.964286
11 1IP CYS PHE SER LYS PRO ARG 0.539062 0.80597
12 ALA PHE ARG ILE PRO LEU THR ARG 0.535433 0.80597
13 GLY ASP CYS PHE SER LYS PRO ARG 0.534884 0.84375
14 0G6 0.534653 0.883333
15 TYR PRO LYS ARG ILE ALA 0.532787 0.830769
16 TYR PRO TYR 0.532609 0.770492
17 TYR MET ASP PHE ASP ASP ASP ILE PRO PHE 0.526316 0.810345
18 ILE ARG ALA ALA PRO PRO PRO LEU PHE 0.515625 0.84375
19 ARG ARG LEU PRO ILE PHE SER ARG LEU 0.507692 0.80597
20 ARG PRO PRO GLY PHE 0.504425 0.881356
21 ARG PRO PRO GLY PHE SER PRO PHE ARG 0.504425 0.881356
22 ARG PRO PRO ILE PHE ILE ARG ARG LEU 0.503876 0.857143
23 LEU PRO PHE ASP ARG THR THR ILE MET 0.50365 0.75
24 LYS PRO LYS 0.494505 0.836364
25 PHE PRO ARG PRO TRP LEU HIS GLY LEU 0.489933 0.794118
26 LEU PRO PHE GLU ARG ALA THR VAL MET 0.485915 0.771429
27 SER PRO LYS ARG ILE ALA 0.482456 0.825397
28 ACE PRO ALA PRO PHE 0.48 0.754098
29 LEU PRO PHE GLU ARG ALA THR ILE MET 0.479167 0.760563
30 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.478261 0.818182
31 GLU PRO GLY GLY SER ARG 0.477876 0.83871
32 ALA ILE MET PRO ALA ARG PHE TYR PRO LYS 0.473333 0.75
33 TRP ASP ILE PRO PHE 0.471698 0.770492
34 ARG THR PHE SER PRO THR TYR GLY LEU 0.471014 0.75
35 VAL MET ALA PRO ARG THR LEU PHE LEU 0.471014 0.771429
36 ARG PRO PRO GLY PHE SER PRO PHE ALA 0.470149 0.80303
37 LEU GLN ARG VAL LEU SEP ALA PRO PHE 0.469697 0.771429
38 32U 0.469388 0.859649
39 LEU ASP PRO ARG 0.463636 0.852459
40 THR PRO PRO SER PRO PHE 0.462963 0.75
41 ARG SEP PRO VAL PHE SER 0.462121 0.768116
42 LEU PRO PHE GLU LEU ARG GLY HIS LEU VAL 0.462069 0.830769
43 ASP LEU PRO PHE 0.458716 0.770492
44 ARG PRO LYS ARG ILE ALA 0.458333 0.852459
45 GLY SER ASP PRO PHE LYS 0.456897 0.761905
46 VAL PRO PRO PRO ARG PRO PRO PRO PRO GLU 0.45614 0.866667
47 ARG MET PHE PRO ASN ALA PRO TYR LEU 0.455172 0.701299
48 PRO PHQ PHE 0.453608 0.779661
49 ARG PRO GLN VAL PRO LEU ARG PRO MET 0.450382 0.776119
50 ALA ASN SER ARG PHE PRO THR SER ILE ILE 0.45 0.794118
51 ALA THR PRO PHE GLN GLU 0.45 0.758065
52 ARG PRO MET THR PHE LYS GLY ALA LEU 0.449664 0.760563
53 GLN PRO PRO VAL PRO PRO GLN ARG PRO MET 0.442748 0.776119
54 ASN PRO ARG ALA MET GLN ALA LEU LEU 0.44186 0.764706
55 TYR PRO SER LYS PRO ASP ASN PRO GLY GLU 0.440367 0.723077
56 ARG GLN PHE GLY PRO ASP PHE PRO THR ILE 0.439189 0.771429
57 MAA LYS PRO PHE 0.4375 0.779661
58 PHE PRO THR LYS ASP VAL ALA LEU 0.437037 0.716418
59 ALA DAL PRO PHE NIT 0.433628 0.638889
60 PHE ASN PHE PRO GLN ILE THR 0.433071 0.681159
61 LYS THR PHE PRO PRO THR GLU PRO LYS 0.432836 0.727273
62 ARG PRO PRO LYS PRO ARG PRO ARG 0.432203 0.877193
63 VAL PRO LEU ARG PRO MET THR TYR 0.431655 0.739726
64 GLY PRO ARG PRO 0.431373 0.862069
65 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.430769 0.736111
66 ARG PHE PRO LEU THR PHE GLY TRP 0.430464 0.760563
67 TRP PRO TRP 0.429907 0.783333
68 5JP PRO LYS ARG ILE ALA 0.429752 0.8
69 ACE GLN GLU ARG GLU VAL PRO CYS 0.42623 0.83871
70 J5K 0.425743 0.703125
71 06P 0.424242 0.737705
72 P05 0.424242 0.745763
73 ARG PRO LYS PRO LEU VAL ASP PRO 0.423729 0.806452
74 ASN TYR THR PRO GLY PRO GLY THR ARG PHE 0.422819 0.760563
75 GLU PHE SER PRO 0.420561 0.8
76 ARG TYR PRO LEU THR PHE GLY TRP 0.420382 0.739726
77 DTY ILE ARG LEU LPD 0.419355 0.815385
78 VAL MET ALA PRO ARG ALA LEU LEU LEU 0.417323 0.8
79 LEU PRO SER PHE GLU THR ALA LEU 0.416667 0.716418
80 99P 0.415842 0.733333
81 ARG ILE ILE PRO ARG HIS LEU GLN LEU 0.415493 0.80303
82 ALA PRO PRO PRO ARG PRO PRO LYS PRO 0.415254 0.847458
83 PHE GLN PRO GLN ASN GLY GLN PHE ILE 0.414815 0.727273
84 ASP TYR ASN PRO TYR LEU LEU PHE LEU LYS 0.414815 0.666667
85 PHE LEU TRP GLY PRO ARG ALA LEU VAL 0.414474 0.818182
86 ASN TYR THR PRO GLY PRO GLY ILE ARG PHE 0.414474 0.739726
87 SER ALA PRO ASP THR ARG PRO ALA 0.414062 0.764706
88 ACE PRO ALA PRO PHE ALA ALA ALA ALA NH2 0.413462 0.704918
89 SER PRO ILE VAL PRO SER PHE ASP MET 0.413043 0.657534
90 ASN ARG PRO ILE LEU SER LEU 0.412698 0.764706
91 ILE GLY PRO GLY ARG ALA PHE TYR ALA 0.412587 0.80597
92 TYR PRO ASN VAL ASN ILE HIS ASN PHE 0.412587 0.648649
93 ILE ARG TYR PRO LYS THR PHE GLY TRP 0.412121 0.739726
94 22U 0.411765 0.721311
95 PHE SER HIS PRO GLN ASN THR 0.411765 0.710145
96 B03 0.411765 0.745763
97 ARG PRO GLY ASN PHE LEU GLN SER ARG PRO 0.410959 0.768116
98 LYS PRO VAL LEU ARG THR ALA 0.410853 0.8
99 ARG PRO GLY ASN PHE LEU GLN SER ARG LEU 0.410596 0.779412
100 ALA TRP ARG HIS PRO GLN PHE GLY GLY 0.410256 0.84375
101 ARG PRO ARG PRO ASP ASP LEU GLU ILE 0.409091 0.8
102 ALA MET ALA PRO ARG THR LEU LEU LEU 0.407692 0.742857
103 PHE LEU PRO SER ASP PHE PHE PRO SER VAL 0.407692 0.685714
104 ASP VAL GLN THR GLY ARG ARG PRO TYR GLU 0.406897 0.782609
105 GOZ 0.405941 0.692308
106 ASN ARG PRO VAL TYR ILE PRO ARG PRO PRO 0.405797 0.791045
107 S49 0.405405 0.675676
108 THR PRO ARG ARG SER MLZ SER ALA 0.404959 0.728571
109 PAC DLY DLY DAR 0.403846 0.77193
110 MIN 0.403846 0.745763
111 10P 0.403846 0.714286
112 LEU ASN PHE PRO ILE SER PRO 0.403226 0.685714
113 ARG GLN PRO ALA LYS ALA PRO LEU LEU 0.402985 0.8125
114 VAL PRO LEU 0.402174 0.775862
115 51U 0.401961 0.758621
116 GLY PHE GLU PRO 0.401869 0.857143
117 AZL 0.401786 0.738462
118 3A2 0.401709 0.681159
119 ILE GLY PRO GLY ARG ALA PHE TYR VAL 0.401361 0.794118
120 ILE GLY PRO GLY ARG ALA PHE TYR THR 0.401361 0.794118
121 PRO LYS ARG PRO THR THR LEU ASN LEU PHE 0.401316 0.768116
Similar Ligands (3D)
Ligand no: 1; Ligand: DPN PRO ARG; Similar ligands found: 1
No: Ligand Similarity coefficient
1 J3I 0.8748
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3VXE; Ligand: DPN PRO ARG; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 3vxe.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1OSS BEN 47.0852
2 1SQA UI1 47.3469
3 6A8N CYS PRO ALA TYR SER ARG TYR ILE GLY CYS 48.1781
4 1FIW PBZ 49.0347
5 1PQ7 ARG 49.5536
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