FAIRMol

MK164

Pose ID 3635 Compound 2643 Pose 249

DB fairmolDocking 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 MK164
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
50.7 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.76, Jaccard 0.70, H-bond role recall 0.50
Burial
89%
Hydrophobic fit
75%
Reason: 6 internal clashes, strain 50.7 kcal/mol
strain ΔE 50.7 kcal/mol 6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Acceptable LE (-0.233 kcal/mol/HA) ✓ Good fit quality (FQ -2.42) ✓ Good H-bonds (3 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Extreme strain energy (50.7 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (8) ✗ Many internal clashes (26)
Score
-9.102
kcal/mol
LE
-0.233
kcal/mol/HA
Fit Quality
-2.42
FQ (Leeson)
HAC
39
heavy atoms
MW
527
Da
LogP
5.01
cLogP
Strain ΔE
50.7 kcal/mol
SASA buried
89%
Lipo contact
75% BSA apolar/total
SASA unbound
765 Ų
Apolar buried
510 Ų

Interaction summary

HB 3 HY 24 PI 3 CLASH 6

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 rank3.458Score-9.102
Inter norm-0.605Intra norm0.285
Top1000noExcludedno
Contacts18H-bonds3
Artifact reasongeometry warning; 26 clashes; 8 protein contact clashes; high strain Δ 50.7
Residues
ALA34 ARG59 ASP54 GLN56 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 PRO91 THR184 TYR166 TYR57 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 overlap16Native recall0.76
Jaccard0.70RMSD-
HB strict2Strict recall0.40
HB same residue+role2HB role recall0.50
HB same residue2HB residue recall0.50

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
231 2.5146509302570808 -0.649378 -23.2854 4 16 1 0.05 0.00 - no Open
249 3.457946757372318 -0.604996 -9.10158 3 18 16 0.76 0.50 - no Current
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 -9.102kcal/mol
Ligand efficiency (LE) -0.2334kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -2.422
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) 50.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 122.05kcal/mol
Minimised FF energy 71.32kcal/mol

SASA & burial

✓ computed
SASA (unbound) 764.9Ų
Total solvent-accessible surface area of free ligand
BSA total 682.1Ų
Buried surface area upon binding
BSA apolar 510.3Ų
Hydrophobic contacts buried
BSA polar 171.8Ų
Polar contacts buried
Fraction buried 89.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1824.5Ų
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 576.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)