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 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....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 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 181 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: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 1 1
2 G 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 GCP 0.765432 0.960526
11 G1R 0.765432 0.973333
12 GDP MG 0.7625 0.935065
13 GAV 0.759036 0.948052
14 GSP 0.756098 0.935897
15 GNP 0.756098 0.960526
16 GDP BEF 0.753086 0.911392
17 ALF 5GP 0.753086 0.9
18 GMP 0.732394 0.866667
19 GTP MG 0.72619 0.935065
20 BEF GDP 0.72619 0.9
21 GPG 0.724138 0.948052
22 GCP G 0.717647 0.947368
23 G2R 0.712644 0.948052
24 GDP AF3 0.701149 0.9
25 GDP ALF 0.701149 0.9
26 Y9Z 0.692308 0.890244
27 GDC 0.692308 0.948052
28 GKE 0.692308 0.948052
29 GDD 0.692308 0.948052
30 YGP 0.681319 0.9125
31 G G 0.677778 0.947368
32 G3A 0.677419 0.960526
33 G5P 0.670213 0.960526
34 GFB 0.666667 0.948052
35 GDR 0.666667 0.948052
36 GTG 0.666667 0.924051
37 6CK 0.659574 0.924051
38 3GP 0.65 0.959459
39 GKD 0.645833 0.948052
40 JB2 0.645833 0.948052
41 GPD 0.639175 0.9125
42 GDX 0.639175 0.960526
43 GDP 7MG 0.635417 0.923077
44 G3D 0.617977 0.972973
45 U2G 0.617647 0.924051
46 IMP 0.609756 0.972603
47 2GP 0.609756 0.946667
48 JB3 0.607843 0.935897
49 CG2 0.605769 0.924051
50 G4P 0.604396 0.972973
51 DGP 0.60241 0.922078
52 DG 0.60241 0.922078
53 FEG 0.601942 0.890244
54 NGD 0.601942 0.948052
55 ZGP 0.596154 0.879518
56 0O2 0.595745 0.972973
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 G A A A 0.579439 0.935065
61 U A G G 0.574074 0.947368
62 MGD 0.568807 0.879518
63 DBG 0.566372 0.935897
64 PGD 0.5625 0.9125
65 MD1 0.5625 0.879518
66 P2G 0.55814 0.894737
67 FE9 0.553571 0.784946
68 I2C FE2 CMO CMO 0.54955 0.818182
69 P1G 0.545455 0.883117
70 GH3 0.542553 0.96
71 TPG 0.53913 0.829545
72 GPX 0.53125 0.933333
73 DGI 0.527473 0.910256
74 G1R G1R 0.525862 0.911392
75 PGD O 0.521368 0.83908
76 DGT 0.521277 0.910256
77 G4M 0.520325 0.869048
78 G G U 0.519231 0.947368
79 G C 0.513514 0.911392
80 93A 0.511364 0.821429
81 IDP 0.505495 0.959459
82 MGQ 0.505155 0.948052
83 C2R 0.5 0.893333
84 BGO 0.5 0.911392
85 AMP 0.5 0.905405
86 AMZ 0.5 0.905405
87 A 0.5 0.905405
88 AIR 0.493671 0.890411
89 MGV 0.49 0.901235
90 SGP 0.488889 0.8375
91 U G A 0.488189 0.9
92 NIA 0.488095 0.8375
93 GPC 0.474138 0.890244
94 G G G RPC 0.473684 0.886076
95 GGM 0.473684 0.888889
96 71V 0.47191 0.85
97 APC G U 0.470085 0.897436
98 MGP 0.46875 0.948052
99 C2E 0.468085 0.933333
100 35G 0.468085 0.945946
101 PCG 0.468085 0.945946
102 G1G 0.466102 0.9125
103 7RA 0.465909 0.918919
104 AAM 0.465909 0.905405
105 RMB 0.465909 0.813333
106 FAI 0.465909 0.905405
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 P2P 0.433333 0.842105
124 JLN 0.433333 0.88
125 XMP 0.428571 0.907895
126 PGS 0.425532 0.804878
127 RVP 0.423529 0.84
128 G2Q 0.423077 0.948052
129 ADP 0.419355 0.906667
130 A2D 0.417582 0.881579
131 ABM 0.417582 0.857143
132 GUO 0.415842 0.932432
133 CA0 0.410526 0.883117
134 2SA 0.41 0.871795
135 1YD 0.409091 0.933333
136 4BW 0.409091 0.933333
137 AP2 0.408602 0.871795
138 A12 0.408602 0.871795
139 BA3 0.408602 0.881579
140 6C6 0.408163 0.825
141 25A 0.407767 0.906667
142 NOS 0.406977 0.813333
143 AMP MG 0.406593 0.833333
144 ATP 0.40625 0.906667
145 AP5 0.404255 0.881579
146 B4P 0.404255 0.881579
147 6IA 0.40404 0.785714
148 ACQ 0.40404 0.883117
149 ANP 0.40404 0.883117
150 CGP 0.403361 0.878049
151 3ZE 0.402062 0.871795
152 APC 0.402062 0.871795
153 5FA 0.402062 0.906667
154 AQP 0.402062 0.906667
155 N6P 0.4 0.853333
156 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: 162
This union binding pocket(no: 1) in the query (biounit: 3py5.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NU4 MLA 0.0003232 0.51212 None
2 1BTN I3P 0.0009267 0.50585 None
3 1UO5 PIH 0.03758 0.41267 None
4 3F81 STT 0.01489 0.4118 None
5 2XBP ATP 0.01004 0.41163 None
6 1H8G CHT 0.04434 0.4087 None
7 1Y42 TYR 0.004423 0.41176 1.09489
8 3QV9 QV7 0.007162 0.40842 1.45985
9 2YIV NBN 0.003997 0.43173 1.82482
10 2YIV YIV 0.01172 0.41676 1.82482
11 1NML CIT 0.00445 0.41165 1.82482
12 2YD6 FLC 0.001376 0.50297 1.88679
13 1A5V Y3 0.009254 0.40371 1.89873
14 3UEC ALA ARG TPO LYS 0.01045 0.41271 2.05479
15 1V7R CIT 0.03848 0.4046 2.15054
16 3IHB TRS 0.0002484 0.5782 2.18978
17 4C6F NCD 0.0009769 0.42688 2.18978
18 4C6F DOR 0.0009769 0.42688 2.18978
19 3IHB GLU 0.01116 0.4114 2.18978
20 4JWX 1N4 0.005833 0.40685 2.18978
21 4RJK PYR 0.02038 0.4053 2.18978
22 2CE7 ADP 0.002341 0.40297 2.18978
23 2O66 FLC 0.009773 0.4027 2.22222
24 1HFA PIO 0.0000698 0.53064 2.55474
25 3LTW HLZ 0.002323 0.4355 2.55474
26 1GJW GLC 0.01459 0.40608 2.55474
27 2P69 PLP 0.009876 0.40251 2.55474
28 4NAO AKG 0.01835 0.40151 2.55474
29 3I51 45C 0.00003664 0.47437 2.59259
30 1Y1A GSH 0.02492 0.42807 2.73224
31 1DL7 NCH 0.0344 0.41479 2.75229
32 3WCS MAN NAG 0.007007 0.40359 2.75591
33 2BR6 HSL 0.00009432 0.45736 2.77778
34 3TKA CTN 0.003448 0.46896 2.91971
35 2XVE FAD 0.006076 0.4307 2.91971
36 2JFV FLC 0.003707 0.42661 2.91971
37 1I0Z OXM 0.0115 0.42415 2.91971
38 2ZE3 AKG 0.005193 0.41433 2.91971
39 3I7S PYR 0.02029 0.40539 2.91971
40 3P47 CYS 0.005325 0.40343 2.91971
41 4K7O EKZ 0.002544 0.44066 2.97619
42 3CBG 4FE 0.01781 0.4221 3.01724
43 2QIA U20 0.0202 0.40393 3.05344
44 1XX4 BAM 0.03306 0.40129 3.06513
45 4KCT PYR 0.0001612 0.46337 3.20641
46 1GVF PGH 0.00189 0.42684 3.28467
47 1O68 KIV 0.002349 0.42298 3.28467
48 1T3D CYS 0.006707 0.42149 3.28467
49 4WBD ADP 0.007101 0.42036 3.28467
50 3SHR CMP 0.003717 0.4047 3.28467
51 2XUM OGA 0.01495 0.4 3.28467
52 2VKL MLT 0.01291 0.42936 3.33333
53 1NF8 BOG 0.003583 0.43389 3.38164
54 3FIU POP 0.02015 0.40444 3.61446
55 1SQ5 ADP 0.00006075 0.46624 3.64964
56 2BO4 FLC 0.001279 0.45423 3.64964
57 1R27 MGD 0.001556 0.43407 3.64964
58 2IZ1 ATR 0.003294 0.42886 3.64964
59 3L6R MLI 0.008108 0.41774 3.64964
60 3MAG 3MA 0.02702 0.41265 3.64964
61 4CIB 7UZ 0.009419 0.40338 3.64964
62 4DYO SD4 0.005903 0.40166 3.64964
63 1H8P PC 0.001789 0.46409 3.66972
64 1ZUW DGL 0.004915 0.40481 3.67647
65 3R51 MMA 0.004466 0.44447 3.75
66 1QH5 GBP 0.02108 0.40295 3.84615
67 1QH9 LAC 0.00436 0.42352 3.87931
68 2VQ5 HBA 0.01224 0.40957 3.9801
69 2VQ5 LDP 0.03426 0.40052 3.9801
70 2V5E SCR 0.001571 0.47668 4
71 1PTR PRB 0.01086 0.41194 4
72 4B9E FAH 0.002156 0.44393 4.0146
73 1KC7 PPR 0.01761 0.40773 4.0146
74 2ZJ5 ADP 0.009642 0.40295 4.0146
75 2B7N NTM 0.011 0.40052 4.0293
76 2BZ1 TAU 0.01861 0.42943 4.08163
77 2QDT I38 0.0000256 0.46702 4.08922
78 2WGC SIA GAL BGC 0.01629 0.43259 4.09357
79 1W3R PYR 0.005151 0.4337 4.16667
80 1W3R 2MN 0.002396 0.4026 4.16667
81 3U1T MLI 0.01904 0.40079 4.20712
82 2C31 TZD 0.003838 0.44481 4.37956
83 1PEA ACM 0.003228 0.44331 4.37956
84 2C31 ADP 0.004046 0.44323 4.37956
85 1H0C AOA 0.00742 0.41949 4.37956
86 3FPZ AHZ 0.02121 0.41586 4.37956
87 3EYK EYK 0.01473 0.40028 4.65116
88 2P1E LAC 0.00002253 0.56428 4.74453
89 3AHC TPP 0.00455 0.40873 4.74453
90 3UDG TMP 0.0258 0.40669 4.74453
91 3CQ5 PMP 0.005537 0.40276 4.74453
92 1QRD DQN 0.02407 0.40184 4.7619
93 2GDZ NAD 0.005257 0.40636 4.86891
94 4K6B GLU 0.01137 0.41417 4.96894
95 3ZPG 5GP 0.0008932 0.47898 5.10949
96 9LDB OXM 0.02156 0.41778 5.10949
97 9LDT OXM 0.02758 0.41219 5.10949
98 1WHT BZS 0.007344 0.41358 5.22876
99 4OHB 5HM 0.001621 0.40422 5.26316
100 1IG3 VIB 0.01352 0.41249 5.32319
101 1M2X MCO 0.0006124 0.48074 5.38117
102 1HQL GLA MBG 0.004107 0.43119 5.44747
103 1H16 DTL 0.01464 0.41894 5.47445
104 2ZO9 MLI 0.001744 0.41472 5.47445
105 1GPJ CIT 0.01258 0.4033 5.47445
106 4LO6 SIA GAL 0.009703 0.41734 5.78947
107 4M5P MLA 0.00143 0.47879 5.83942
108 4O8A 2OP 0.001188 0.47287 5.83942
109 1ULE GLA GAL NAG 0.00933 0.42146 6
110 3KJQ B94 0.002198 0.40854 6.09756
111 4EXO PYR 0.01191 0.41642 6.16438
112 4LFL TG6 0.002131 0.41393 6.39535
113 3PNA CMP 0.0004564 0.44554 6.49351
114 2X2T GAL NGA 0.00008792 0.52863 6.53595
115 2Q8H TF4 0.01235 0.4226 6.56934
116 1JAC AMG 0.0001559 0.52846 6.76692
117 3NNF AKG 0.009355 0.40897 6.93431
118 2XRH NIO 0.001458 0.45165 7
119 1JN2 SFP 0.01982 0.41256 7.173
120 1Y9Q MED 0.003455 0.42795 7.29167
121 4ME6 ADP 0.0001658 0.4775 7.29927
122 3ZY6 GFB 0.001626 0.41253 7.29927
123 3WUD GLC GAL 0.01463 0.41217 7.35294
124 4AF5 CIT 0.01456 0.40051 7.36842
125 1OIK AKG 0.003296 0.42884 7.66423
126 2Z9V PXM 0.006218 0.40571 7.66423
127 1SC3 MLI 0.006242 0.42974 7.95455
128 1JGS SAL 0.003181 0.47118 7.97101
129 3L24 GOA 0.003584 0.44919 8.0292
130 4F8L GAL 0.02731 0.4203 8.27586
131 1ZED PNP 0.01123 0.41128 8.39416
132 3S9K CIT 0.01282 0.43564 8.47458
133 2Y6P CTP 0.00323 0.40703 8.54701
134 4U9W SER GLY ARG GLY LYS NH2 0.009565 0.40576 8.69565
135 2CW6 3HG 0.01589 0.41718 8.75912
136 1NNS ASP 0.001865 0.41614 8.75912
137 1TUV VK3 0.0004478 0.49377 8.77193
138 1Y7P RIP 0.004342 0.4236 8.96861
139 1Z42 HBA 0.01156 0.44774 9.12409
140 4JLV ADP 0.012 0.43528 9.29368
141 3QDW A2G 0.003322 0.45083 9.79021
142 3QDT A2G GAL 0.0173 0.4087 9.79021
143 3QDY CBS 0.01847 0.40139 9.79021
144 1RZM E4P 0.01293 0.40847 9.85401
145 1OGD RIP 0.004326 0.41215 9.92366
146 3SCH TB6 0.002958 0.4309 10.101
147 2FGQ MLT 0.01257 0.40332 10.219
148 1ZZ7 S0H 0.005707 0.40723 10.6061
149 4N7C AEF 0.0038 0.43273 10.7955
150 4TYT S3C 0.0007218 0.47437 11.0132
151 1G8S MET 0.01012 0.40747 11.3043
152 3PMA SCR 0.007575 0.4022 11.583
153 2W3L DRO 0.02222 0.40992 11.8056
154 1NP0 NGT 0.002324 0.43549 12.1053
155 2DWU DGL 0.004743 0.40542 12.4088
156 1Z0N BCD 0.02432 0.41648 12.5
157 2ZWS PLM 0.008379 0.44833 13.8686
158 1F1V DHY 0.001702 0.42299 14.2336
159 4K30 NLG 0.004947 0.40977 15
160 3E5P PPI 0.03356 0.40236 16.0584
161 1M1B SPV 0.004737 0.41602 19.708
162 4O4Z N2O 0.01078 0.42156 25.3247
Feedback