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Receptor
PDB id Resolution Class Description Source Keywords
3MD7 1.27 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF A BETA-LACTAMASE-LIKE PROTEIN BOUND TO BRUCELLA MELITENSIS BRUCELLA MELITENSIS BIOVAR ABORTUS SSGCID BETA-LACTAMASE LIKE HYDROLASE STRUCTURAL GENOMICSSTRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Ref.: BRABA.11339.A: ANOMALOUS DIFFRACTION AND LIGAND BIN GUIDE TOWARDS THE ELUCIDATION OF THE FUNCTION OF A BETA-LACTAMASE-LIKE PROTEIN FROM BRUCELLA MELITENSI ACTA CRYSTALLOGR.,SECT.F V. 67 1106 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP A:303;
Valid;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
K A:302;
Part of Protein;
none;
submit data
39.098 K [K+]
MN A:300;
A:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
NA A:305;
A:306;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
TLA A:304;
Invalid;
none;
submit data
150.087 C4 H6 O6 [C@@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PY5 1.7 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF A BETA-LACTAMASE-LIKE PROTEIN FROM BRUC MELITENSIS BOUND TO AMP BRUCELLA MELITENSIS BIOVAR ABORTUS SSGCID BETA-LACTAMASE LIKE BRUCELLA MELITENSIS GMP AMP CENTRE STRUCTURAL GENOMICS SEATTLE STRUCTURAL GENOMICS CEINFECTIOUS DISEASE HYDROLASE
Ref.: BRABA.11339.A: ANOMALOUS DIFFRACTION AND LIGAND BIN GUIDE TOWARDS THE ELUCIDATION OF THE FUNCTION OF A BETA-LACTAMASE-LIKE PROTEIN FROM BRUCELLA MELITENSI ACTA CRYSTALLOGR.,SECT.F V. 67 1106 2011
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 3MD7 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3QH8 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 3PY6 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
4 3PY5 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 3MD7 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3QH8 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 3PY6 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
4 3PY5 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 3MD7 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 3QH8 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 3PY6 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
4 3PY5 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP; Similar ligands found: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 G 1 1
2 5GP 1 1
3 GDP 0.828947 0.986486
4 GP3 0.815789 0.960526
5 GP2 0.805195 0.948052
6 GTP 0.797468 0.986486
7 GNH 0.794872 0.973333
8 G2P 0.777778 0.948052
9 GMV 0.775 0.960526
10 G1R 0.765432 0.973333
11 GCP 0.765432 0.960526
12 GAV 0.759036 0.948052
13 GSP 0.756098 0.935897
14 GNP 0.756098 0.960526
15 9GM 0.756098 0.960526
16 ALF 5GP 0.753086 0.9
17 GMP 0.732394 0.866667
18 GPG 0.724138 0.948052
19 G2R 0.712644 0.948052
20 ALF GDP 0.701149 0.9
21 GDP ALF 0.701149 0.9
22 GDP AF3 0.701149 0.9
23 GKE 0.692308 0.948052
24 Y9Z 0.692308 0.890244
25 GDC 0.692308 0.948052
26 GDD 0.692308 0.948052
27 YGP 0.681319 0.9125
28 G3A 0.677419 0.960526
29 G5P 0.670213 0.960526
30 GFB 0.666667 0.948052
31 GDR 0.666667 0.948052
32 GTG 0.666667 0.924051
33 6CK 0.659574 0.924051
34 3GP 0.65 0.959459
35 G G 0.648936 0.960526
36 GKD 0.645833 0.948052
37 JB2 0.645833 0.948052
38 GDX 0.639175 0.960526
39 GPD 0.639175 0.9125
40 GDP 7MG 0.635417 0.923077
41 G3D 0.617977 0.972973
42 U2G 0.617647 0.924051
43 2GP 0.609756 0.946667
44 IMP 0.609756 0.972603
45 JB3 0.607843 0.935897
46 CG2 0.605769 0.924051
47 G4P 0.604396 0.972973
48 DGP 0.60241 0.922078
49 DG 0.60241 0.922078
50 FEG 0.601942 0.890244
51 NGD 0.601942 0.948052
52 ZGP 0.596154 0.879518
53 0O2 0.595745 0.972973
54 2MD 0.584906 0.879518
55 G7M 0.583333 0.960526
56 CAG 0.583333 0.869048
57 G A A A 0.579439 0.935065
58 A G 0.579439 0.947368
59 U A G G 0.574074 0.947368
60 MGD 0.568807 0.879518
61 DBG 0.566372 0.935897
62 PGD 0.5625 0.9125
63 MD1 0.5625 0.879518
64 P2G 0.55814 0.894737
65 GCP G 0.556701 0.933333
66 FE9 0.553571 0.784946
67 P1G 0.545455 0.883117
68 GH3 0.542553 0.96
69 TPG 0.53913 0.829545
70 GPX 0.53125 0.933333
71 DGI 0.527473 0.910256
72 G1R G1R 0.525862 0.911392
73 G U 0.522936 0.911392
74 PGD O 0.521368 0.83908
75 DGT 0.521277 0.910256
76 G4M 0.520325 0.869048
77 AKW 0.513761 0.878049
78 G C 0.513514 0.911392
79 93A 0.511364 0.821429
80 IDP 0.505495 0.959459
81 MGQ 0.505155 0.948052
82 C2R 0.5 0.893333
83 A 0.5 0.905405
84 AMZ 0.5 0.905405
85 BGO 0.5 0.911392
86 AMP 0.5 0.905405
87 AIR 0.493671 0.890411
88 MGV 0.49 0.901235
89 SGP 0.488889 0.8375
90 NIA 0.488095 0.8375
91 GPC 0.474138 0.890244
92 G G G RPC 0.473684 0.886076
93 GGM 0.473684 0.888889
94 71V 0.47191 0.85
95 APC G U 0.470085 0.897436
96 R5I 0.46875 0.933333
97 R7I 0.46875 0.933333
98 MGP 0.46875 0.948052
99 35G 0.468085 0.945946
100 PCG 0.468085 0.945946
101 C2E 0.468085 0.933333
102 G1G 0.466102 0.9125
103 AAM 0.465909 0.905405
104 RMB 0.465909 0.813333
105 FAI 0.465909 0.905405
106 7RA 0.465909 0.918919
107 1RB 0.465116 0.824324
108 6G0 0.463918 0.948052
109 5GP 5GP 0.463158 0.894737
110 G G G C 0.462185 0.924051
111 RBZ 0.45977 0.815789
112 UCG 0.459016 0.923077
113 A G C C 0.458333 0.923077
114 DG DG 0.456311 0.876543
115 G U34 0.45614 0.9
116 IMO 0.449438 0.866667
117 A G U 0.446154 0.9
118 G C C C 0.443548 0.935897
119 IRN 0.443038 0.808219
120 PMO 0.43956 0.792208
121 7RP 0.438202 0.864865
122 GTA 0.436364 0.924051
123 JLN 0.433333 0.88
124 P2P 0.433333 0.842105
125 A G U U 0.42963 0.9
126 XMP 0.428571 0.907895
127 PGS 0.425532 0.804878
128 RVP 0.423529 0.84
129 G2Q 0.423077 0.948052
130 ADP 0.419355 0.906667
131 ABM 0.417582 0.857143
132 A2D 0.417582 0.881579
133 PRT 0.416667 0.945946
134 GUO 0.415842 0.932432
135 AT4 0.414894 0.871795
136 CA0 0.410526 0.883117
137 2SA 0.41 0.871795
138 1YD 0.409091 0.933333
139 4BW 0.409091 0.933333
140 A12 0.408602 0.871795
141 AP2 0.408602 0.871795
142 BA3 0.408602 0.881579
143 6C6 0.408163 0.825
144 25A 0.407767 0.906667
145 NOS 0.406977 0.813333
146 HEJ 0.40625 0.906667
147 ATP 0.40625 0.906667
148 AP5 0.404255 0.881579
149 B4P 0.404255 0.881579
150 ACQ 0.40404 0.883117
151 6IA 0.40404 0.785714
152 ANP 0.40404 0.883117
153 CGP 0.403361 0.878049
154 APC 0.402062 0.871795
155 3ZE 0.402062 0.871795
156 5FA 0.402062 0.906667
157 AQP 0.402062 0.906667
158 N6P 0.4 0.853333
159 AN2 0.4 0.894737
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PY5; Ligand: AMP; Similar sites found with APoc: 26
This union binding pocket(no: 1) in the query (biounit: 3py5.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5FJJ MAN 2.55474
2 2BR6 HSL 2.77778
3 4KVL PLM 2.91971
4 5GVL GI8 2.91971
5 5GVL PLG 2.91971
6 6CGZ HL6 3.28467
7 3FIU POP 3.61446
8 5U97 PIT 4.0146
9 1KC7 PPR 4.0146
10 2QDT I38 4.08922
11 2P1E LAC 4.74453
12 3NB0 G6P 4.74453
13 4K6B GLU 4.96894
14 1M2X MCO 5.38117
15 5OCQ CIT 5.47445
16 5Z5I XYP 5.47445
17 5HIP 61O 5.47445
18 5E5U MLI 5.68182
19 4EXS X8Z 6.25
20 5EW0 3C7 6.83761
21 5NM7 GLY 7.5188
22 6EW3 S3C 9.05172
23 4G9N NGA 10.4895
24 1WRA PC 11.6788
25 5AHO TLA 17.8832
26 4O4Z N2O 25.3247
Pocket No.: 2; Query (leader) PDB : 3PY5; Ligand: AMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3py5.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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