FAIRMol

MK179

Pose ID 330 Compound 234 Pose 330

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
T01
Human DHFR Human
Ligand MK179
PDB5SD8↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
41.5 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.00
Burial
85%
Hydrophobic fit
59%
Reason: 10 internal clashes
10 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.860 kcal/mol/HA) ✓ Good fit quality (FQ -8.29) ✓ Deep burial (85% SASA buried) ✗ Extreme strain energy (41.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-25.797
kcal/mol
LE
-0.860
kcal/mol/HA
Fit Quality
-8.29
FQ (Leeson)
HAC
30
heavy atoms
MW
458
Da
LogP
2.66
cLogP
Strain ΔE
41.5 kcal/mol
SASA buried
85%
Lipo contact
59% BSA apolar/total
SASA unbound
690 Ų
Apolar buried
343 Ų

Interaction summary

HB 2 HY 24 PI 2 CLASH 0
Final rank1.623Score-25.797
Inter norm-0.921Intra norm0.061
Top1000noExcludedno
Contacts18H-bonds2
Artifact reasongeometry warning; 10 clashes; 1 protein clash; high strain Δ 41.5
Residues
ALA10 ARG29 ASN65 GLU31 ILE61 ILE8 LEU23 LEU28 LEU68 NAP201 PHE32 PHE35 PRO27 PRO62 THR137 TYR122 VAL116 VAL9

Protein summary

200 residues
Protein targetT01Atoms3128
Residues200Chains2
Residue summaryLYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

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:NAP201

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5SD8Contacts21
PoseOpen native poseHB0
IFP residues
ALA10 ASN65 ASP22 GLN36 GLU31 GLY117 GLY21 ILE61 ILE8 LEU23 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9
Current overlap15Native recall0.71
Jaccard0.62RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
258 0.25042243857344604 -1.14891 -31.0205 5 13 0 0.00 0.00 - no Open
264 1.0927050169268024 -1.00795 -24.7925 4 14 0 0.00 0.00 - no Open
235 1.1073660704846975 -0.900181 -23.0605 5 17 0 0.00 0.00 - no Open
257 1.107384658545134 -0.819468 -19.7407 2 17 0 0.00 0.00 - no Open
313 1.3452488083914984 -0.690473 -17.5537 4 16 0 0.00 0.00 - no Open
252 1.4292786430260862 -0.917081 -25.3234 6 21 0 0.00 0.00 - no Open
330 1.622607140224942 -0.920565 -25.7973 2 18 15 0.71 0.00 - no Current
281 1.8373311043657956 -0.808595 -21.8267 3 15 0 0.00 0.00 - no Open
206 1.8644199550012546 -0.798056 -18.2624 8 14 0 0.00 0.00 - no Open
361 2.311042942916434 -0.848092 -25.1719 4 12 0 0.00 0.00 - no Open
261 2.5727308749693383 -0.803338 -20.2039 2 12 0 0.00 0.00 - no Open
224 2.7169060620044525 -1.02158 -27.5832 9 18 0 0.00 0.00 - no Open
234 3.995775267533372 -1.22318 -34.5475 13 21 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 -25.797kcal/mol
Ligand efficiency (LE) -0.8599kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.295
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.66
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 90.22kcal/mol
Minimised FF energy 48.72kcal/mol

SASA & burial

✓ computed
SASA (unbound) 689.6Ų
Total solvent-accessible surface area of free ligand
BSA total 583.2Ų
Buried surface area upon binding
BSA apolar 343.0Ų
Hydrophobic contacts buried
BSA polar 240.2Ų
Polar contacts buried
Fraction buried 84.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 58.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1506.2Ų
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 1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 614.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)