Receptor
PDB id Resolution Class Description Source Keywords
4DXD 2.01 Å NON-ENZYME: CELL_CYCLE STAPHYLOCOCCAL AUREUS FTSZ IN COMPLEX WITH 723 STAPHYLOCOCCUS AUREUS ROSSMANN FOLD GTPASE GTP BINDING CELL CYCLE-INHIBITOR COM
Ref.: RESTORING METHICILLIN-RESISTANT STAPHYLOCOCCUS AURE SUSCEPTIBILITY TO BETA-LACTAM ANTIBIOTICS. SCI TRANSL MED V. 4 6RA35 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
9PC A:402;
Valid;
none;
submit data
355.747 C14 H8 Cl F2 N3 O2 S c1cc(...
GDP A:401;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DXD 2.01 Å NON-ENZYME: CELL_CYCLE STAPHYLOCOCCAL AUREUS FTSZ IN COMPLEX WITH 723 STAPHYLOCOCCUS AUREUS ROSSMANN FOLD GTPASE GTP BINDING CELL CYCLE-INHIBITOR COM
Ref.: RESTORING METHICILLIN-RESISTANT STAPHYLOCOCCUS AURE SUSCEPTIBILITY TO BETA-LACTAM ANTIBIOTICS. SCI TRANSL MED V. 4 6RA35 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 4DXD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3WGM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 4DXD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3WGM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 2RHL - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 2RHO - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 5XDV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5XDT - MB3 C5 H9 N O CN1CCCC1=O
7 5H5G - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 5H5H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 5H5I - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 5XDW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 5MN4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 5XDU - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 4DXD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3WGM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 2RHL - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 2RHO - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 5XDV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 5XDT - MB3 C5 H9 N O CN1CCCC1=O
7 5H5G - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 5H5H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 5H5I - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 5XDW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 5MN4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 5XDU - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 1W5F - G2P C11 H18 N5 O13 P3 c1nc2c(n1[....
14 1RQ2 ic50 = 3 mM CIT C6 H8 O7 C(C(=O)O)C....
15 1RLU - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
16 1W5B - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 1W5A - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
18 1W58 - G2P C11 H18 N5 O13 P3 c1nc2c(n1[....
19 2VAP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 2R6R - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 2R75 Kd = 714 nM 01G C14 H23 N6 O15 P3 C1COCCN1c2....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 9PC; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 9PC 1 1
2 ZI7 0.693333 0.945455
Ligand no: 2; Ligand: GDP; Similar ligands found: 153
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 GNP 0.839506 0.973684
6 G 0.828947 0.986486
7 5GP 0.828947 0.986486
8 G1R 0.82716 0.986667
9 GCP 0.82716 0.973684
10 GSP 0.817073 0.948718
11 GAV 0.797619 0.961039
12 GMV 0.792683 0.973684
13 G2P 0.77381 0.961039
14 G2R 0.770115 0.961039
15 GDP MG 0.759036 0.923077
16 GP2 0.756098 0.961039
17 GDP BEF 0.75 0.9
18 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GDC 0.747253 0.961039
21 GPG 0.741573 0.961039
22 G3D 0.732558 0.986486
23 ALF 5GP 0.729412 0.888889
24 Y9Z 0.728261 0.902439
25 GTP MG 0.724138 0.923077
26 BEF GDP 0.724138 0.888889
27 G5P 0.723404 0.973684
28 GFB 0.72043 0.961039
29 GTG 0.72043 0.936709
30 GDR 0.72043 0.961039
31 G4P 0.715909 0.986486
32 GCP G 0.715909 0.935065
33 6CK 0.712766 0.936709
34 G3A 0.712766 0.973684
35 GDP ALF 0.7 0.888889
36 GDP AF3 0.7 0.888889
37 YGP 0.698925 0.901235
38 JB2 0.697917 0.961039
39 GKD 0.697917 0.961039
40 GDX 0.690722 0.973684
41 GPD 0.690722 0.925
42 GMP 0.684211 0.88
43 0O2 0.666667 0.986486
44 G G 0.659574 0.935065
45 JB3 0.656863 0.948718
46 NGD 0.650485 0.961039
47 GDP 7MG 0.636364 0.911392
48 DGI 0.636364 0.923077
49 U2G 0.634615 0.936709
50 GPX 0.634409 0.946667
51 IDP 0.632184 0.972973
52 2MD 0.632075 0.891566
53 CAG 0.62963 0.880952
54 CG2 0.622642 0.936709
55 FEG 0.619048 0.879518
56 MGD 0.614679 0.891566
57 ZGP 0.613208 0.869048
58 GH3 0.612903 0.973333
59 3GP 0.611765 0.946667
60 MD1 0.607143 0.891566
61 PGD 0.59292 0.925
62 DGT 0.591398 0.923077
63 BGO 0.588785 0.924051
64 TPG 0.582609 0.840909
65 DBG 0.582609 0.948718
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 I2C FE2 CMO CMO 0.566372 0.808989
69 G A A A 0.553571 0.923077
70 MGP 0.553191 0.961039
71 U A G G 0.548673 0.935065
72 G4M 0.548387 0.880952
73 6G0 0.547368 0.961039
74 G1R G1R 0.542373 0.924051
75 P2G 0.527473 0.883117
76 PGD O 0.525 0.850575
77 ADP 0.522222 0.92
78 GGM 0.517544 0.901235
79 DG 0.516484 0.910256
80 DGP 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G G U 0.509259 0.935065
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 G C 0.504348 0.9
86 GPC 0.491525 0.879518
87 G7M 0.483871 0.948052
88 6AD 0.479592 0.841463
89 ATP 0.473684 0.92
90 G2Q 0.471154 0.961039
91 U G A 0.469697 0.888889
92 5FA 0.46875 0.92
93 AQP 0.46875 0.92
94 GTA 0.468468 0.936709
95 7DD 0.468085 0.906667
96 G G G RPC 0.466102 0.875
97 SGP 0.463158 0.82716
98 01G 0.462963 0.902439
99 B4P 0.457447 0.894737
100 AP5 0.457447 0.894737
101 A2D 0.456522 0.894737
102 G G G C 0.455285 0.9125
103 ACQ 0.454545 0.896104
104 5GP 5GP 0.454545 0.883117
105 ANP 0.454545 0.896104
106 A G C C 0.451613 0.911392
107 APC G U 0.45082 0.886076
108 G U34 0.449153 0.888889
109 DG DG 0.448598 0.865854
110 ITT 0.447917 0.868421
111 BA3 0.446809 0.894737
112 35G 0.444444 0.933333
113 C2E 0.444444 0.921053
114 PCG 0.444444 0.933333
115 MGO 0.441176 0.864198
116 AN2 0.4375 0.907895
117 G C C C 0.4375 0.924051
118 M33 0.43299 0.883117
119 UCG 0.429688 0.911392
120 A G U 0.42963 0.888889
121 ACP 0.428571 0.896104
122 MGQ 0.424528 0.935897
123 7DT 0.424242 0.906667
124 APR 0.424242 0.894737
125 AR6 0.424242 0.894737
126 93A 0.42268 0.833333
127 A4P 0.420168 0.869048
128 SAP 0.42 0.873418
129 AD9 0.42 0.896104
130 AGS 0.42 0.873418
131 G8D 0.42 0.875
132 CA0 0.418367 0.896104
133 ATF 0.417476 0.884615
134 AGO 0.414634 0.888889
135 NIA 0.413043 0.82716
136 MGV 0.412844 0.890244
137 TAT 0.411765 0.884615
138 A1R 0.411215 0.839506
139 ADQ 0.411215 0.871795
140 RGT 0.410714 0.909091
141 CGP 0.409836 0.86747
142 AMP 0.408602 0.893333
143 A 0.408602 0.893333
144 UP5 0.40678 0.873418
145 C2R 0.406593 0.906667
146 AMZ 0.406593 0.918919
147 JBT 0.405882 0.778947
148 A22 0.40566 0.907895
149 25L 0.405405 0.907895
150 ADX 0.40404 0.809524
151 8OD 0.401961 0.946667
152 4TC 0.4 0.851852
153 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DXD; Ligand: 9PC; Similar sites found: 50
This union binding pocket(no: 1) in the query (biounit: 4dxd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ZB6 GST 0.00635 0.41304 1.76768
2 4P8K 38C 0.03677 0.40281 2.08333
3 4P8K FAD 0.0357 0.40281 2.08333
4 5TUF TDC 0.01173 0.42681 2.27273
5 4ANW O92 0.007914 0.41138 2.27273
6 5HCY 60D 0.02075 0.40281 2.27273
7 1Q9I FAD 0.02474 0.40987 2.27671
8 1Q9I TEO 0.02474 0.40987 2.27671
9 4LO2 GAL BGC 0.003045 0.46999 2.36486
10 3L9R L9R 0.01363 0.4064 2.4735
11 5DEY 59T 0.02394 0.40637 2.6936
12 2A2C NG1 0.01865 0.40406 2.92887
13 2A2C ADP 0.01865 0.40406 2.92887
14 3KRR DQX 0.03395 0.40511 3.0303
15 5DQ8 FLF 0.007233 0.41185 3.33333
16 1S4M LUM 0.007788 0.40637 3.41297
17 5N2D 8J8 0.002486 0.4124 3.47222
18 1HDR NAD 0.006152 0.43348 3.68852
19 1OUK 084 0.04332 0.41492 3.82514
20 1KGI T4A 0.004844 0.41075 3.93701
21 5N2F 8HW 0.0006129 0.44753 4.03226
22 5J8O 6GZ 0.000458 0.43069 4.03226
23 4MIB 28M 0.03079 0.4107 4.29293
24 3TAY MN0 0.002336 0.42608 4.29448
25 4OYA 1VE 0.03421 0.40555 4.54545
26 2RCU BUJ 0.01341 0.41982 4.79798
27 4WO4 JLS 0.01214 0.41171 4.79798
28 4L2I NAD 0.009769 0.42068 4.94297
29 1LSH PLD 0.002322 0.43233 5.30303
30 5AE2 FAD 0.03728 0.40822 5.30303
31 5AE2 FYC 0.03728 0.40822 5.30303
32 4MNS 2AX 0.02611 0.4023 6.28931
33 3ZNN FAD 0.03468 0.40278 6.34006
34 3ZNN 4WL 0.03468 0.40278 6.34006
35 5A89 FMN 0.01032 0.41687 6.41026
36 5A89 ADP 0.01032 0.41687 6.41026
37 3QCQ 3Q0 0.04908 0.40663 6.73077
38 5A5W GUO 0.01787 0.40399 7.11462
39 3IX8 TX3 0.001534 0.43565 7.51445
40 2AG4 LP3 0.01176 0.42609 8.53659
41 2AG4 OLA 0.0239 0.40926 8.53659
42 1NHX PEP 0.02318 0.40057 8.83838
43 5B4B LP5 0.01198 0.40083 9.67742
44 2WLG SOP 0.02187 0.40897 10.101
45 3OKI OKI 0.01839 0.40341 10.3004
46 2I0D MUT 0.01694 0.42104 11.1111
47 1NB9 ADP 0.01481 0.40578 12.2449
48 1NB9 RBF 0.01481 0.40578 12.2449
49 4NG2 OHN 0.005054 0.41156 24.7788
50 3LKJ LKJ 0.006565 0.415 30.4965
Pocket No.: 2; Query (leader) PDB : 4DXD; Ligand: GDP; Similar sites found: 23
This union binding pocket(no: 2) in the query (biounit: 4dxd.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3M89 GSP 0.0000001753 0.49728 2.10773
2 1COY AND 0.01196 0.41151 2.27273
3 1COY FAD 0.007221 0.40962 2.27273
4 1XHL NDP 0.006362 0.40221 2.6936
5 2BTO GTP 0.000000006097 0.62394 4.62963
6 4LNU GTP 0.00000002958 0.6074 4.73373
7 4LNU GDP 0.00000008479 0.56628 4.73373
8 3CB2 GDP 0.00000007125 0.53551 6.31313
9 1H2B NAJ 0.003447 0.41431 6.56566
10 3ZBQ GDP 0.0000003137 0.53235 9.09091
11 3RYC GTP 0.000000005269 0.64721 11.9101
12 5EYP GDP 0.000000007803 0.63298 11.9101
13 5LXT GTP 0.0000002963 0.62461 11.9101
14 5LXT GDP 0.000001339 0.60699 11.9101
15 5LXT 7AK 0.000001239 0.60699 11.9101
16 5EIB GTP 0.00000003423 0.60488 11.9101
17 5ITZ GTP 0.00000005803 0.59577 11.9101
18 5EYP GTP 0.00000006457 0.59393 11.9101
19 5ITZ GDP 0.00000003482 0.5881 11.9101
20 3RYC GDP 0.00000008606 0.57991 11.9101
21 1UWK NAD 0.01116 0.40517 13.6364
22 1UWK URO 0.01116 0.40517 13.6364
23 4EI7 GDP 0.0000000128 0.60368 18.509
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