FAIRMol

ulfkktlib_3745

Pose ID 1612 Compound 1326 Pose 257

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
T03
L. major DHFR L. major
Ligand ulfkktlib_3745

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
66.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.65, Jaccard 0.52, H-bond role recall 0.20
Burial
79%
Hydrophobic fit
82%
Reason: strain 66.9 kcal/mol
strain ΔE 66.9 kcal/mol 1 protein-contact clashes 46% of hydrophobic surface appears solvent-exposed (13/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.715 kcal/mol/HA) ✓ Good fit quality (FQ -7.42) ✓ Good H-bonds (4 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Extreme strain energy (66.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-27.883
kcal/mol
LE
-0.715
kcal/mol/HA
Fit Quality
-7.42
FQ (Leeson)
HAC
39
heavy atoms
MW
531
Da
LogP
2.44
cLogP
Final rank
2.7098
rank score
Inter norm
-0.747
normalised
Contacts
18
H-bonds 4
Strain ΔE
66.9 kcal/mol
SASA buried
79%
Lipo contact
82% BSA apolar/total
SASA unbound
919 Ų
Apolar buried
599 Ų

Interaction summary

HBA 4 HY 6 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap13Native recall0.65
Jaccard0.52RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; 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
155 2.5629984015001437 -0.747059 -27.525 16 15 0 0.00 0.00 - no Open
257 2.7097506770575244 -0.747384 -27.883 4 18 13 0.65 0.20 - no Current
251 4.443560184982545 -0.50084 -17.9358 8 13 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 -27.883kcal/mol
Ligand efficiency (LE) -0.7149kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.420
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 39HA

Physicochemical properties
Molecular weight 530.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.44
Lipinski: ≤ 5
Rotatable bonds 11

Conformational strain (MMFF94s)
Strain energy (ΔE) 66.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 99.59kcal/mol
Minimised FF energy 32.68kcal/mol

SASA & burial

✓ computed
SASA (unbound) 919.4Ų
Total solvent-accessible surface area of free ligand
BSA total 725.5Ų
Buried surface area upon binding
BSA apolar 598.9Ų
Hydrophobic contacts buried
BSA polar 126.6Ų
Polar contacts buried
Fraction buried 78.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1766.3Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 823.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)