FAIRMol

MK33

Pose ID 321 Compound 395 Pose 321

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
T01
Human DHFR Human
Ligand MK33
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
48.3 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.67, Jaccard 0.56, H-bond role recall 0.40
Burial
81%
Hydrophobic fit
88%
Reason: 14 internal clashes, strain 48.3 kcal/mol
strain ΔE 48.3 kcal/mol 14 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.695 kcal/mol/HA) ✓ Good fit quality (FQ -6.83) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Extreme strain energy (48.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-22.238
kcal/mol
LE
-0.695
kcal/mol/HA
Fit Quality
-6.83
FQ (Leeson)
HAC
32
heavy atoms
MW
462
Da
LogP
2.78
cLogP
Final rank
2.3191
rank score
Inter norm
-0.843
normalised
Contacts
18
H-bonds 3
Strain ΔE
48.3 kcal/mol
SASA buried
81%
Lipo contact
88% BSA apolar/total
SASA unbound
788 Ų
Apolar buried
564 Ų

Interaction summary

HBD 1 HBA 1 HY 10 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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.

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 overlap14Native recall0.67
Jaccard0.56RMSD-
HB strict2Strict recall0.40
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
321 2.3190664543888877 -0.843483 -22.2376 3 18 14 0.67 0.40 - no Current
302 3.741445713545639 -0.604967 -16.2823 8 11 0 0.00 0.00 - no Open
244 3.8180782023918276 -0.830247 -17.9078 4 17 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 -22.238kcal/mol
Ligand efficiency (LE) -0.6949kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.834
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 461.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 48.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 78.37kcal/mol
Minimised FF energy 30.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 787.8Ų
Total solvent-accessible surface area of free ligand
BSA total 637.2Ų
Buried surface area upon binding
BSA apolar 564.1Ų
Hydrophobic contacts buried
BSA polar 73.1Ų
Polar contacts buried
Fraction buried 80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1759.9Ų
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 601.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)