Receptor
PDB id Resolution Class Description Source Keywords
4MCQ 2 Å EC: 3.4.17.21 A HIGH RESOLUTION STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTID (GCPII) IN COMPLEX WITH FOLYLDI-GAMMA-L-GLUTAMIC ACID (PTERG AMMA-L-GLUTAMIC ACID) HOMO SAPIENS HYDROLASE METALLOPEPTIDASE HYDROLASE-HYDROLASE INHIBITOR CPROSTATE SPECIFIC MEMBRANE ANTIGEN FOLATE HYDROLASE 1 FOL
Ref.: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE FOLYL-POLY-GAMMA-L-GLUTAMATE HYDROLYZING ACTIVITY O GLUTAMATE CARBOXYPEPTIDASE II. FEBS J. V. 281 3228 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
29C A:818;
Valid;
none;
submit data
699.625 C29 H33 N9 O12 c1cc(...
ZN A:802;
A:801;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
NAG NAG A:812;
A:808;
A:805;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
408.404 n/a O=C(N...
NAG NAG BMA MAN A:814;
Invalid;
none;
submit data
732.686 n/a O=C(N...
NAG A:807;
A:811;
A:810;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
CA A:803;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
CL A:804;
Invalid;
none;
submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4X3R 1.86 Å EC: 3.4.17.21 AVI-GCPII STRUCTURE IN COMPLEX WITH FITC-CONJUGATED GCPII-SP INHIBITOR HOMO SAPIENS GLYCOPROTEIN METALLOPEPTIDASE INHIBITOR HYDROLASE
Ref.: DESIGN OF HIGHLY POTENT UREA-BASED, EXOSITE-BINDING INHIBITORS SELECTIVE FOR GLUTAMATE CARBOXYPEPTIDASE J.MED.CHEM. V. 58 4357 2015
Members (45)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3D7F ic50 = 0.5 nM YBY C15 H17 I N2 O8 c1cc(c(cc1....
2 3BI0 ic50 = 14 nM BIX C10 H18 N O8 P C(CC(=O)O)....
3 4OC3 Ki = 5.3 nM 2QP C21 H24 I N3 O7 c1cc(oc1)C....
4 4MCR - 29D C34 H40 N10 O15 c1cc(ccc1C....
5 2XEF Ki = 0.145 nM AR8 C37 H60 N8 O19 c1cc(c(cc1....
6 4OC2 Ki = 5.3 nM 2QQ C19 H22 I N3 O6 C#CC[C@@H]....
7 2PVV ic50 = 438 uM OSE C3 H7 N O6 S C([C@@H](C....
8 2PVW ic50 = 0.3 nM G88 C6 H11 O7 P C(CC(=O)O)....
9 4OC1 Ki = 254 nM 2QS C19 H24 I N3 O7 c1cc(ccc1C....
10 4P4D ic50 = 1800 nM 2GR C14 H19 N2 O8 P c1ccc(cc1)....
11 4MCS - ASP C4 H7 N O4 C([C@@H](C....
12 3SJE - SDR C15 H26 N2 O6 CCCCCCC[C@....
13 4X3R Ki = 0.0086 nM 686 C60 H59 Br N8 O14 c1cc(ccc1C....
14 4P4J ic50 = 700 nM 2H9 C15 H19 N2 O10 P c1ccc(cc1)....
15 3D7D ic50 = 14 nM FBD C16 H19 F N2 O7 S c1cc(ccc1C....
16 4OC5 Ki = 85 nM 2QM C22 H24 I N3 O7 c1cc(ccc1[....
17 2C6C ic50 = 30 nM 24I C13 H16 I O6 P c1cc(ccc1C....
18 4P4B ic50 = 14 nM 2G2 C13 H22 N3 O12 P C(CC(=O)N[....
19 3D7G ic50 = 17 nM MUD C10 H16 N2 O7 S CSC[C@@H](....
20 3SJF Ki = 29 nM JRG C19 H26 I N3 O6 S CSCC[C@@H]....
21 3BI1 ic50 = 0.12 nM 3BI C25 H31 N8 O9 P C[N@](Cc1c....
22 4P4I ic50 = 35 nM 2G5 C15 H19 N2 O10 P c1ccc(cc1)....
23 4P44 ic50 = 16 nM 2F7 C21 H29 F N3 O11 P CC[C@@H](C....
24 5D29 ic50 = 97 nM 5Q1 C13 H15 N O6 c1cc(ccc1C....
25 3SJG - SDR C15 H26 N2 O6 CCCCCCC[C@....
26 5F09 - BC8 C11 H15 N O10 C(CC(=O)O)....
27 4P4F ic50 = 168 nM 2GB C18 H20 N O7 P c1ccc(cc1)....
28 4MCQ - 29C C29 H33 N9 O12 c1cc(ccc1C....
29 2XEG Ki = 0.02 nM CI9 C29 H46 N8 O15 c1cc(c(cc1....
30 2OR4 ic50 = 9.5 uM QUS C5 H7 N3 O5 C([C@@H](C....
31 2XEJ Ki = 1.34 nM OKD C24 H41 N5 O12 COCCOCCOCC....
32 4P45 ic50 = 16 nM 2F9 C20 H27 F N3 O11 P CC(C)[C@@H....
33 3D7H ic50 = 0.06 nM YC2 C19 H24 I N3 O8 c1cc(ccc1C....
34 4P4E ic50 = 180 nM 2G4 C15 H22 N O7 P c1ccc(cc1)....
35 2JBJ Ki = 0.2 nM G88 C6 H11 O7 P C(CC(=O)O)....
36 2XEI Ki = 0.024 nM ARK C25 H36 N8 O13 c1cc(c(cc1....
37 3BXM - ACE ASP GLU n/a n/a
38 3BHX ic50 = 0.7 nM BHX C9 H15 O8 P C(CC(=O)O)....
39 4OC4 Ki = 105 nM 2QN C22 H25 I N4 O6 c1cc(ccc1C....
40 5ELY ic50 = 44 nM 5PU C13 H15 N O6 c1cc(ccc1C....
41 4OC0 Ki = 318 nM 2R7 C18 H22 I N3 O6 c1cc(ccc1C....
42 4MCP - 28Z C24 H26 N8 O9 c1cc(ccc1C....
43 3SJX - QRG C11 H18 N2 O6 S CC(=O)N[C@....
44 3IWW Ki = 11 nM YZE C19 H24 I N3 O6 C=CC[C@@H]....
45 3RBU Ki = 370 pM G88 C6 H11 O7 P C(CC(=O)O)....
70% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3D7F ic50 = 0.5 nM YBY C15 H17 I N2 O8 c1cc(c(cc1....
2 3BI0 ic50 = 14 nM BIX C10 H18 N O8 P C(CC(=O)O)....
3 4OC3 Ki = 5.3 nM 2QP C21 H24 I N3 O7 c1cc(oc1)C....
4 4MCR - 29D C34 H40 N10 O15 c1cc(ccc1C....
5 2XEF Ki = 0.145 nM AR8 C37 H60 N8 O19 c1cc(c(cc1....
6 4OC2 Ki = 5.3 nM 2QQ C19 H22 I N3 O6 C#CC[C@@H]....
7 2PVV ic50 = 438 uM OSE C3 H7 N O6 S C([C@@H](C....
8 2PVW ic50 = 0.3 nM G88 C6 H11 O7 P C(CC(=O)O)....
9 4OC1 Ki = 254 nM 2QS C19 H24 I N3 O7 c1cc(ccc1C....
10 4P4D ic50 = 1800 nM 2GR C14 H19 N2 O8 P c1ccc(cc1)....
11 4MCS - ASP C4 H7 N O4 C([C@@H](C....
12 3SJE - SDR C15 H26 N2 O6 CCCCCCC[C@....
13 4X3R Ki = 0.0086 nM 686 C60 H59 Br N8 O14 c1cc(ccc1C....
14 4P4J ic50 = 700 nM 2H9 C15 H19 N2 O10 P c1ccc(cc1)....
15 3D7D ic50 = 14 nM FBD C16 H19 F N2 O7 S c1cc(ccc1C....
16 4OC5 Ki = 85 nM 2QM C22 H24 I N3 O7 c1cc(ccc1[....
17 2C6C ic50 = 30 nM 24I C13 H16 I O6 P c1cc(ccc1C....
18 4P4B ic50 = 14 nM 2G2 C13 H22 N3 O12 P C(CC(=O)N[....
19 3D7G ic50 = 17 nM MUD C10 H16 N2 O7 S CSC[C@@H](....
20 3SJF Ki = 29 nM JRG C19 H26 I N3 O6 S CSCC[C@@H]....
21 3BI1 ic50 = 0.12 nM 3BI C25 H31 N8 O9 P C[N@](Cc1c....
22 4P4I ic50 = 35 nM 2G5 C15 H19 N2 O10 P c1ccc(cc1)....
23 4P44 ic50 = 16 nM 2F7 C21 H29 F N3 O11 P CC[C@@H](C....
24 5D29 ic50 = 97 nM 5Q1 C13 H15 N O6 c1cc(ccc1C....
25 3SJG - SDR C15 H26 N2 O6 CCCCCCC[C@....
26 5F09 - BC8 C11 H15 N O10 C(CC(=O)O)....
27 4P4F ic50 = 168 nM 2GB C18 H20 N O7 P c1ccc(cc1)....
28 4MCQ - 29C C29 H33 N9 O12 c1cc(ccc1C....
29 2XEG Ki = 0.02 nM CI9 C29 H46 N8 O15 c1cc(c(cc1....
30 2OR4 ic50 = 9.5 uM QUS C5 H7 N3 O5 C([C@@H](C....
31 2XEJ Ki = 1.34 nM OKD C24 H41 N5 O12 COCCOCCOCC....
32 4P45 ic50 = 16 nM 2F9 C20 H27 F N3 O11 P CC(C)[C@@H....
33 3D7H ic50 = 0.06 nM YC2 C19 H24 I N3 O8 c1cc(ccc1C....
34 4P4E ic50 = 180 nM 2G4 C15 H22 N O7 P c1ccc(cc1)....
35 2JBJ Ki = 0.2 nM G88 C6 H11 O7 P C(CC(=O)O)....
36 2XEI Ki = 0.024 nM ARK C25 H36 N8 O13 c1cc(c(cc1....
37 3BXM - ACE ASP GLU n/a n/a
38 3BHX ic50 = 0.7 nM BHX C9 H15 O8 P C(CC(=O)O)....
39 4OC4 Ki = 105 nM 2QN C22 H25 I N4 O6 c1cc(ccc1C....
40 5ELY ic50 = 44 nM 5PU C13 H15 N O6 c1cc(ccc1C....
41 4OC0 Ki = 318 nM 2R7 C18 H22 I N3 O6 c1cc(ccc1C....
42 4MCP - 28Z C24 H26 N8 O9 c1cc(ccc1C....
43 3SJX - QRG C11 H18 N2 O6 S CC(=O)N[C@....
44 3IWW Ki = 11 nM YZE C19 H24 I N3 O6 C=CC[C@@H]....
45 3RBU Ki = 370 pM G88 C6 H11 O7 P C(CC(=O)O)....
46 3FEE Ki = 230 nM QUS C5 H7 N3 O5 C([C@@H](C....
47 3FED Ki = 34.6 nM BIX C10 H18 N O8 P C(CC(=O)O)....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3D7F ic50 = 0.5 nM YBY C15 H17 I N2 O8 c1cc(c(cc1....
2 3BI0 ic50 = 14 nM BIX C10 H18 N O8 P C(CC(=O)O)....
3 4OC3 Ki = 5.3 nM 2QP C21 H24 I N3 O7 c1cc(oc1)C....
4 4MCR - 29D C34 H40 N10 O15 c1cc(ccc1C....
5 2XEF Ki = 0.145 nM AR8 C37 H60 N8 O19 c1cc(c(cc1....
6 4OC2 Ki = 5.3 nM 2QQ C19 H22 I N3 O6 C#CC[C@@H]....
7 2PVV ic50 = 438 uM OSE C3 H7 N O6 S C([C@@H](C....
8 2PVW ic50 = 0.3 nM G88 C6 H11 O7 P C(CC(=O)O)....
9 4OC1 Ki = 254 nM 2QS C19 H24 I N3 O7 c1cc(ccc1C....
10 4P4D ic50 = 1800 nM 2GR C14 H19 N2 O8 P c1ccc(cc1)....
11 4MCS - ASP C4 H7 N O4 C([C@@H](C....
12 3SJE - SDR C15 H26 N2 O6 CCCCCCC[C@....
13 4X3R Ki = 0.0086 nM 686 C60 H59 Br N8 O14 c1cc(ccc1C....
14 4P4J ic50 = 700 nM 2H9 C15 H19 N2 O10 P c1ccc(cc1)....
15 3D7D ic50 = 14 nM FBD C16 H19 F N2 O7 S c1cc(ccc1C....
16 4OC5 Ki = 85 nM 2QM C22 H24 I N3 O7 c1cc(ccc1[....
17 2C6C ic50 = 30 nM 24I C13 H16 I O6 P c1cc(ccc1C....
18 4P4B ic50 = 14 nM 2G2 C13 H22 N3 O12 P C(CC(=O)N[....
19 3D7G ic50 = 17 nM MUD C10 H16 N2 O7 S CSC[C@@H](....
20 3SJF Ki = 29 nM JRG C19 H26 I N3 O6 S CSCC[C@@H]....
21 3BI1 ic50 = 0.12 nM 3BI C25 H31 N8 O9 P C[N@](Cc1c....
22 4P4I ic50 = 35 nM 2G5 C15 H19 N2 O10 P c1ccc(cc1)....
23 4P44 ic50 = 16 nM 2F7 C21 H29 F N3 O11 P CC[C@@H](C....
24 5D29 ic50 = 97 nM 5Q1 C13 H15 N O6 c1cc(ccc1C....
25 3SJG - SDR C15 H26 N2 O6 CCCCCCC[C@....
26 5F09 - BC8 C11 H15 N O10 C(CC(=O)O)....
27 4P4F ic50 = 168 nM 2GB C18 H20 N O7 P c1ccc(cc1)....
28 4MCQ - 29C C29 H33 N9 O12 c1cc(ccc1C....
29 2XEG Ki = 0.02 nM CI9 C29 H46 N8 O15 c1cc(c(cc1....
30 2OR4 ic50 = 9.5 uM QUS C5 H7 N3 O5 C([C@@H](C....
31 2XEJ Ki = 1.34 nM OKD C24 H41 N5 O12 COCCOCCOCC....
32 4P45 ic50 = 16 nM 2F9 C20 H27 F N3 O11 P CC(C)[C@@H....
33 3D7H ic50 = 0.06 nM YC2 C19 H24 I N3 O8 c1cc(ccc1C....
34 4P4E ic50 = 180 nM 2G4 C15 H22 N O7 P c1ccc(cc1)....
35 2JBJ Ki = 0.2 nM G88 C6 H11 O7 P C(CC(=O)O)....
36 2XEI Ki = 0.024 nM ARK C25 H36 N8 O13 c1cc(c(cc1....
37 3BXM - ACE ASP GLU n/a n/a
38 3BHX ic50 = 0.7 nM BHX C9 H15 O8 P C(CC(=O)O)....
39 4OC4 Ki = 105 nM 2QN C22 H25 I N4 O6 c1cc(ccc1C....
40 5ELY ic50 = 44 nM 5PU C13 H15 N O6 c1cc(ccc1C....
41 4OC0 Ki = 318 nM 2R7 C18 H22 I N3 O6 c1cc(ccc1C....
42 4MCP - 28Z C24 H26 N8 O9 c1cc(ccc1C....
43 3SJX - QRG C11 H18 N2 O6 S CC(=O)N[C@....
44 3IWW Ki = 11 nM YZE C19 H24 I N3 O6 C=CC[C@@H]....
45 3RBU Ki = 370 pM G88 C6 H11 O7 P C(CC(=O)O)....
46 3FEE Ki = 230 nM QUS C5 H7 N3 O5 C([C@@H](C....
47 3FED Ki = 34.6 nM BIX C10 H18 N O8 P C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 29C; Similar ligands found: 22
No: Ligand ECFP6 Tc MDL keys Tc
1 28Z 1 1
2 29C 1 1
3 29D 1 1
4 FOL 0.617647 0.967742
5 PD8 0.56 0.75
6 04J 0.495327 0.857143
7 TLL 0.483333 0.776316
8 LYB 0.478261 0.892308
9 9L9 0.475728 0.768116
10 DZF 0.473214 0.951613
11 DHF 0.468468 0.838235
12 3TZ 0.457627 0.838235
13 1YJ 0.452174 0.838235
14 THG 0.452174 0.838235
15 C2F 0.444444 0.75
16 83A 0.443478 0.923077
17 PFG 0.435484 0.852941
18 FFO 0.428571 0.780822
19 DXY 0.421053 0.693333
20 DXZ 0.421053 0.693333
21 GHC 0.410256 0.739726
22 THF 0.408333 0.76
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4X3R; Ligand: 686; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4x3r.bio1) has 59 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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