FAIRMol

MK216

Pose ID 5004 Compound 534 Pose 263

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T08
T. brucei PTR1 T. brucei
Ligand MK216
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
21.6 kcal/mol
Protein clashes
2
Internal clashes
5
Native overlap
contact recall 0.53, Jaccard 0.45, H-bond role recall 0.60
Burial
78%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
2 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.059 kcal/mol/HA) ✓ Good fit quality (FQ -10.21) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (21.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (12)
Score
-31.768
kcal/mol
LE
-1.059
kcal/mol/HA
Fit Quality
-10.21
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
21.6 kcal/mol
SASA buried
78%
Lipo contact
82% BSA apolar/total
SASA unbound
689 Ų
Apolar buried
439 Ų

Interaction summary

HB 11 HY 16 PI 1 CLASH 5
Final rank1.027Score-31.768
Inter norm-1.165Intra norm0.106
Top1000noExcludedno
Contacts13H-bonds11
Artifact reasongeometry warning; 12 clashes; 5 protein contact clashes; 1 severe cofactor-context clash; moderate strain Δ 21.6
Residues
ALA96 ARG14 ASP161 LEU208 LEU209 LYS13 NAP301 PHE97 PRO210 SER95 TYR174 TYR98 VAL211

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NAP301

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap10Native recall0.53
Jaccard0.45RMSD-
HB strict3Strict recall0.50
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
263 1.0267699428225585 -1.16463 -31.7677 11 13 10 0.53 0.60 - no Current
248 1.0565759821753493 -1.05865 -27.2137 11 11 0 0.00 0.00 - no Open
275 1.158072578337196 -0.79049 -20.4723 4 16 0 0.00 0.00 - no Open
326 1.522628122716502 -0.968338 -25.9969 6 13 0 0.00 0.00 - no Open
244 1.708744967754064 -0.825708 -20.6159 5 19 0 0.00 0.00 - no Open
257 1.8345663825114074 -0.798505 -19.855 3 19 0 0.00 0.00 - no Open
309 1.905113599274035 -0.859805 -26.3343 3 12 0 0.00 0.00 - no Open
209 2.4824832058938013 -1.05337 -29.243 13 18 0 0.00 0.00 - no Open
204 2.663282674439042 -1.13906 -30.5138 11 18 0 0.00 0.00 - no Open
270 2.7066301048038337 -0.90359 -23.3047 8 16 0 0.00 0.00 - no Open
335 3.062936325722447 -0.858552 -27.4791 7 19 0 0.00 0.00 - no Open
224 3.0864929722424383 -0.941482 -26.4284 4 18 0 0.00 0.00 - no Open
308 3.1241016565923485 -1.04343 -27.852 6 10 0 0.00 0.00 - no Open
210 3.431812628247348 -1.01323 -26.2551 13 17 0 0.00 0.00 - no Open
200 4.283886601626247 -0.994469 -27.0487 13 17 0 0.00 0.00 - no Open
213 4.298392329825456 -0.999515 -28.3054 11 16 0 0.00 0.00 - no Open
307 4.451695165235262 -0.776336 -19.1475 5 13 0 0.00 0.00 - no Open
249 5.404412263953654 -0.824137 -19.6852 7 12 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -31.768kcal/mol
Ligand efficiency (LE) -1.0589kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.215
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.80
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 53.73kcal/mol
Minimised FF energy 32.11kcal/mol

SASA & burial

✓ computed
SASA (unbound) 688.6Ų
Total solvent-accessible surface area of free ligand
BSA total 537.5Ų
Buried surface area upon binding
BSA apolar 438.9Ų
Hydrophobic contacts buried
BSA polar 98.6Ų
Polar contacts buried
Fraction buried 78.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1688.3Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 948.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)