FAIRMol

MK164

Pose ID 5649 Compound 2643 Pose 231

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
T09
L. major DHFR-TS L. major
Ligand MK164

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 mixed SASA done
Strain ΔE
33.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.52, Jaccard 0.42, H-bond role recall 0.00
Burial
79%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.597 kcal/mol/HA) ✓ Good fit quality (FQ -6.20) ✓ Good H-bonds (4 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (33.1 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (22)
Score
-23.285
kcal/mol
LE
-0.597
kcal/mol/HA
Fit Quality
-6.20
FQ (Leeson)
HAC
39
heavy atoms
MW
527
Da
LogP
5.01
cLogP
Strain ΔE
33.1 kcal/mol
SASA buried
79%
Lipo contact
79% BSA apolar/total
SASA unbound
799 Ų
Apolar buried
499 Ų

Interaction summary

HB 4 HY 24 PI 2 CLASH 2
Final rank2.515Score-23.285
Inter norm-0.649Intra norm0.052
Top1000noExcludedno
Contacts16H-bonds4
Artifact reasongeometry warning; 22 clashes; 5 protein contact clashes; high strain Δ 33.1
Residues
NDP301 ALA32 ARG48 ASP52 ILE45 LYS57 MET53 PHE56 PHE91 PRO50 PRO88 THR54 TRP47 VAL30 VAL31 VAL49

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap11Native recall0.52
Jaccard0.42RMSD-
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
231 2.5146509302570808 -0.649378 -23.2854 4 16 11 0.52 0.00 - no Current
249 3.457946757372318 -0.604996 -9.10158 3 18 1 0.05 0.00 - no Open
193 5.697612732874468 -0.851569 -22.1648 8 22 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 -23.285kcal/mol
Ligand efficiency (LE) -0.5971kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.196
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 39HA

Physicochemical properties
Molecular weight 526.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.01
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 106.19kcal/mol
Minimised FF energy 73.06kcal/mol

SASA & burial

✓ computed
SASA (unbound) 798.6Ų
Total solvent-accessible surface area of free ligand
BSA total 633.5Ų
Buried surface area upon binding
BSA apolar 499.3Ų
Hydrophobic contacts buried
BSA polar 134.2Ų
Polar contacts buried
Fraction buried 79.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3403.3Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1662.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)