Receptor
PDB id Resolution Class Description Source Keywords
3AF0 2.5 Å EC: 2.7.1.33 PANTOTHENATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS (MTPANK) COMPLEX WITH GDP AND PANTOTHENATE MYCOBACTERIUM TUBERCULOSIS TRANSFERASE HOMODIMER COA BIOSYNTHESIS NUCLEOTIDE BINDINGBINDING KINASE NUCLEOTIDE-BINDING
Ref.: M. TUBERCULOSIS PANTOTHENATE KINASE: DUAL SUBSTRATE SPECIFICITY AND UNUSUAL CHANGES IN LIGAND LOCATIONS J.MOL.BIOL. V. 400 171 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:315;
Invalid;
none;
submit data
35.453 Cl [Cl-]
GDP A:313;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
GOL A:316;
A:317;
A:318;
A:319;
A:320;
A:321;
A:322;
A:323;
A:324;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PAU A:314;
Valid;
none;
submit data
219.235 C9 H17 N O5 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4BFW 2.27 Å EC: 2.7.1.33 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANK IN COMPLEX WITH A TRIAZOLE INHIBITORY COMPOUND (1E) AND PHOSPH MYCOBACTERIUM TUBERCULOSIS TRANSFERASE COA PATHWAY
Ref.: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF COMP INHIBITING MYCOBACTERIUM TUBERCULOSIS PANK J.BIOL.CHEM. V. 288 18260 2013
Members (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4BFW ic50 = 0.05 uM ZVW C27 H23 F5 N4 O2 S C[C@@H](c1....
2 4BFU ic50 = 0.15 uM ZVU C20 H18 F4 N4 O S C[C@@H](c1....
3 2GET - COK C23 H40 N7 O17 P3 S2 CC(C)(CO[P....
4 4BFZ ic50 = 0.55 uM ZVZ C26 H27 N5 O2 CNC(=O)COc....
5 3AF1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3AF2 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
7 3AEZ - PAZ C9 H18 N O8 P CC(C)(COP(....
8 4BFV ic50 = 0.14 uM ZVV C22 H23 F3 N4 O2 S Cc1ccccc1O....
9 2ZSD Ka = 212000 M^-1 COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
10 3AF3 - PAU C9 H17 N O5 CC(C)(CO)[....
11 4BFT ic50 = 1.13 uM ZVT C20 H20 Cl F N4 O2 S C[C@@H](c1....
12 2ZSE - FLC C6 H5 O7 C(C(=O)[O-....
13 2ZSA - PAZ C9 H18 N O8 P CC(C)(COP(....
14 4BFY ic50 = 0.12 uM ZVY C25 H24 N4 O3 c1ccnc(c1)....
15 3AF0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 2GEV - COK C23 H40 N7 O17 P3 S2 CC(C)(CO[P....
17 2GES - COK C23 H40 N7 O17 P3 S2 CC(C)(CO[P....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3AF2 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
2 3AEZ - PAZ C9 H18 N O8 P CC(C)(COP(....
3 3AF3 - PAU C9 H17 N O5 CC(C)(CO)[....
4 4BFT ic50 = 1.13 uM ZVT C20 H20 Cl F N4 O2 S C[C@@H](c1....
5 2ZSE - FLC C6 H5 O7 C(C(=O)[O-....
6 2ZSA - PAZ C9 H18 N O8 P CC(C)(COP(....
7 4BFY ic50 = 0.12 uM ZVY C25 H24 N4 O3 c1ccnc(c1)....
8 3AF0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 2GEV - COK C23 H40 N7 O17 P3 S2 CC(C)(CO[P....
10 2GES - COK C23 H40 N7 O17 P3 S2 CC(C)(CO[P....
11 1SQ5 - PAU C9 H17 N O5 CC(C)(CO)[....
12 4NE2 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
13 4GI7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 4F7W - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4BFW ic50 = 0.05 uM ZVW C27 H23 F5 N4 O2 S C[C@@H](c1....
2 4BFU ic50 = 0.15 uM ZVU C20 H18 F4 N4 O S C[C@@H](c1....
3 2GET - COK C23 H40 N7 O17 P3 S2 CC(C)(CO[P....
4 4BFZ ic50 = 0.55 uM ZVZ C26 H27 N5 O2 CNC(=O)COc....
5 3AF1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3AF2 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
7 3AEZ - PAZ C9 H18 N O8 P CC(C)(COP(....
8 4BFV ic50 = 0.14 uM ZVV C22 H23 F3 N4 O2 S Cc1ccccc1O....
9 2ZSD Ka = 212000 M^-1 COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
10 3AF3 - PAU C9 H17 N O5 CC(C)(CO)[....
11 4BFT ic50 = 1.13 uM ZVT C20 H20 Cl F N4 O2 S C[C@@H](c1....
12 2ZSE - FLC C6 H5 O7 C(C(=O)[O-....
13 2ZSA - PAZ C9 H18 N O8 P CC(C)(COP(....
14 4BFY ic50 = 0.12 uM ZVY C25 H24 N4 O3 c1ccnc(c1)....
15 3AF0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 2GEV - COK C23 H40 N7 O17 P3 S2 CC(C)(CO[P....
17 2GES - COK C23 H40 N7 O17 P3 S2 CC(C)(CO[P....
18 1SQ5 - PAU C9 H17 N O5 CC(C)(CO)[....
19 4NE2 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 4GI7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 4F7W - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; 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
Ligand no: 2; Ligand: PAU; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 PAU 1 1
2 PNY 0.604167 0.857143
3 PAZ 0.58 0.811321
4 PCO 0.568627 0.875
5 PN4 0.557692 0.823529
6 ENV 0.517857 0.84
7 ENW 0.5 0.843137
8 0JR 0.453125 0.777778
9 OPI 0.423729 0.86
10 SH2 0.42029 0.704918
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4BFW; Ligand: ZVW; 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: 4bfw.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4BFW; Ligand: ZVW; Similar sites found: 98
This union binding pocket(no: 2) in the query (biounit: 4bfw.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4M9Q GNP 0.002997 0.43506 1.76211
2 4J0Q GDP 0.0001876 0.53211 1.88679
3 1TQ4 GDP 0.001217 0.45637 1.88679
4 3FKQ ATP 0.002323 0.45119 1.88679
5 2ZTS ADP 0.004469 0.43406 1.99203
6 4DKX GDP 0.0005953 0.49963 2.31481
7 3EZ2 ADP 0.007625 0.44677 2.51572
8 4H1V GNP 0.004062 0.43966 2.51572
9 2FNA ADP 0.007483 0.41725 2.51572
10 5BQ5 ADP BEF 0.002516 0.45789 2.6455
11 5DI3 GNP 0.005299 0.42397 2.7027
12 1G7S GDP 0.001177 0.47913 2.83019
13 5VGR GDP 0.001762 0.45689 2.83019
14 4V0K GDP 0.009766 0.40639 2.95858
15 1Z2A GDP 0.008074 0.41281 2.97619
16 3B9Q MLI 0.0003087 0.52156 2.98013
17 2DPY ADP 0.0003541 0.52409 3.14465
18 1YTM ATP 0.008315 0.41827 3.14465
19 4NU0 AP5 0.001801 0.40594 3.22581
20 3BFX A3P 0.00996 0.41782 3.37838
21 1G6O ADP 0.001367 0.47101 3.45912
22 5IRR GSP 0.005004 0.42509 3.57143
23 3GJ0 GDP 0.001139 0.48505 3.61991
24 3N5C GDP 0.0003068 0.51454 3.7037
25 3PCR GTP 0.0009383 0.45391 3.7037
26 5JCP GDP ALF 0.001299 0.46317 3.77358
27 1ZD9 GDP 0.00517 0.43111 3.77358
28 4BQS ADP 0.0006111 0.49904 3.97727
29 3RY9 1CA 0.01961 0.40707 4
30 3BER AMP 0.0202 0.42023 4.01606
31 3GN8 DEX 0.01813 0.40274 4.01606
32 4OHY ANP 0.001712 0.43906 4.08805
33 4NON GDP 0.0003692 0.51037 4.23077
34 4FOU C2E 0.02972 0.40789 4.2735
35 1XEX ATP 0.009879 0.40352 4.65116
36 2A5J GDP 0.001498 0.46904 4.71204
37 1GOJ ADP 0.00004371 0.59059 4.71698
38 4AG5 ADP 0.0002221 0.54041 4.71698
39 4IEE AGS 0.002903 0.46905 4.71698
40 2CK3 ANP 0.002405 0.44658 4.79452
41 2CK3 ADP 0.003945 0.4265 4.79452
42 2WIC GNP 0.0009599 0.4836 4.86891
43 3MBI HSX 0.01417 0.43244 4.87805
44 1S9D GDP 0.0007146 0.49008 4.92611
45 2Y8E GNP 0.005281 0.41508 5.02793
46 4LHW GNP 0.00871 0.40585 5.17241
47 2WKQ GTP 0.005012 0.42193 5.34591
48 4MKG AP5 0.001197 0.40775 5.52995
49 4P4T GDP 0.00413 0.43565 5.66038
50 4Q1A UDP 0.01201 0.41855 5.71429
51 4Q1A 2XZ 0.01201 0.41855 5.71429
52 2YOH WMJ 0.001969 0.41387 5.71429
53 1FNN ADP 0.009674 0.41842 5.9126
54 5TAR GDP 0.0006259 0.48288 5.94595
55 1Z83 AP5 0.001098 0.42345 6.12245
56 4R43 GDP 0.0004831 0.50433 6.28931
57 4QOS ADP 0.001359 0.47114 6.41509
58 2ZFI ADP 0.001099 0.48586 6.55738
59 5FTB ANP 0.001729 0.46596 6.60377
60 5FHD ADP ALF 0.005297 0.42722 6.60377
61 1W7J ADP BEF 0.0009277 0.4701 6.62252
62 5G41 AP5 0.0004991 0.42649 6.72646
63 1TX4 ALF GDP 0.007474 0.41429 6.77966
64 1Z6T ADP 0.000524 0.48187 6.91824
65 1WDT GTP 0.005428 0.43012 7.2327
66 4X8O AP5 0.001116 0.41419 7.47664
67 5W3X IHP 0.02481 0.41942 7.5
68 1GP2 GDP 0.00395 0.42648 7.54717
69 5HR5 FLC 0.0003199 0.40758 7.86164
70 1L2T ATP 0.00141 0.4427 8.08511
71 1AKY AP5 0.002254 0.40248 8.63636
72 3GJ8 GDP 0.001686 0.47122 8.69565
73 2NCD ADP 0.00003881 0.58206 8.80503
74 3LXR GDP 0.00139 0.47064 8.85417
75 1J2J GTP 0.0008913 0.45489 8.88889
76 1U8Z GDP 0.008015 0.41295 8.92857
77 2WJG GDP 0.000328 0.51303 9.57447
78 1HE1 AF3 0.01778 0.43446 9.65909
79 1HE1 GDP 0.006749 0.42241 9.65909
80 3U6B GDP 0.0002429 0.52617 9.74843
81 2BVN GNP 0.001126 0.47052 9.74843
82 1JI0 ATP 0.0001492 0.54448 10
83 2G77 GDP 0.0028 0.44733 10.0629
84 2G77 AF3 0.01425 0.44024 10.0629
85 4CVN ADP 0.00002113 0.5906 10.4712
86 3T12 GDP ALF 0.006749 0.41926 11.7647
87 2HF9 GSP 0.001197 0.46485 11.9469
88 4HI0 GDP 0.0007571 0.46577 12.0603
89 2C04 GCP 0.01562 0.41179 12.4579
90 3TMK T5A 0.00007108 0.41361 13.4259
91 3QBT GNP 0.00642 0.41148 13.5714
92 2CBZ ATP 0.000006348 0.63434 13.9241
93 1GXU 2HP 0.0001533 0.54214 15.3846
94 4LC1 GDP 0.0001861 0.52577 16.3522
95 1M7B GTP 0.00266 0.44088 16.8478
96 2OM2 GDP 0.00269 0.44066 19.4444
97 1UJ2 ADP 0.000001922 0.45708 39.2857
98 1UJ2 C5P 0.000002406 0.45447 39.2857
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