FAIRMol

MK216

Pose ID 3643 Compound 534 Pose 257

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
T06
T. brucei DHFR T. brucei
Ligand MK216
PDB8RHT↗

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
21.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.67, Jaccard 0.54, H-bond role recall 0.00
Burial
93%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.662 kcal/mol/HA) ✓ Good fit quality (FQ -6.38) ✓ Good H-bonds (3 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (21.5 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Many internal clashes (11)
Score
-19.855
kcal/mol
LE
-0.662
kcal/mol/HA
Fit Quality
-6.38
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
21.5 kcal/mol
SASA buried
93%
Lipo contact
83% BSA apolar/total
SASA unbound
683 Ų
Apolar buried
527 Ų

Interaction summary

HB 3 HY 24 PI 4 CLASH 5

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
Final rank1.835Score-19.855
Inter norm-0.799Intra norm0.127
Top1000noExcludedno
Contacts19H-bonds3
Artifact reasongeometry warning; 11 clashes; 9 protein contact clashes; moderate strain Δ 21.5
Residues
ALA34 ARG100 ARG59 ASP54 GLN56 GLU50 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 PRO52 PRO91 TYR166 VAL32 VAL33

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name8RHTContacts21
PoseOpen native poseHB0
IFP residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap14Native recall0.67
Jaccard0.54RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

223 residues
Protein targetT06Atoms3452
Residues223Chains1
Residue summaryARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

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:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
263 1.0267699428225585 -1.16463 -31.7677 11 13 0 0.00 0.00 - no Open
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 14 0.67 0.00 - no Open
257 1.8345663825114074 -0.798505 -19.855 3 19 14 0.67 0.00 - no Current
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 1 0.05 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 -19.855kcal/mol
Ligand efficiency (LE) -0.6618kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.384
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) 21.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 51.00kcal/mol
Minimised FF energy 29.53kcal/mol

SASA & burial

✓ computed
SASA (unbound) 683.1Ų
Total solvent-accessible surface area of free ligand
BSA total 635.7Ų
Buried surface area upon binding
BSA apolar 526.9Ų
Hydrophobic contacts buried
BSA polar 108.8Ų
Polar contacts buried
Fraction buried 93.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1793.5Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 585.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)