FAIRMol

Z31238035

Pose ID 1870 Compound 151 Pose 515

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
T03
L. major DHFR L. major
Ligand Z31238035

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
26.6 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.70, Jaccard 0.61, H-bond role recall 0.20
Burial
92%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.132 kcal/mol/HA) ✓ Good fit quality (FQ -10.14) ✓ Good H-bonds (4 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ High strain energy (26.6 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Internal clashes (6)
Score
-27.166
kcal/mol
LE
-1.132
kcal/mol/HA
Fit Quality
-10.14
FQ (Leeson)
HAC
24
heavy atoms
MW
358
Da
LogP
3.43
cLogP
Strain ΔE
26.6 kcal/mol
SASA buried
92%
Lipo contact
69% BSA apolar/total
SASA unbound
554 Ų
Apolar buried
353 Ų

Interaction summary

HB 4 HY 24 PI 2 CLASH 3
Final rank0.349Score-27.166
Inter norm-1.105Intra norm-0.027
Top1000noExcludedno
Contacts17H-bonds4
Artifact reasongeometry warning; 6 clashes; 4 protein contact clashes; 1 cofactor-context clash; moderate strain Δ 26.6
Residues
ALA32 ASP52 ILE182 ILE45 LEU94 MET53 NDP301 PHE56 PHE91 THR83 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49 VAL87

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

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 overlap14Native recall0.70
Jaccard0.61RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
515 0.3487875686501666 -1.10525 -27.1663 4 17 14 0.70 0.20 - no Current
534 0.42214207708525603 -1.1019 -25.8001 3 16 0 0.00 0.00 - no Open
539 1.2579557912218973 -1.1079 -25.7907 3 16 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 -27.166kcal/mol
Ligand efficiency (LE) -1.1319kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.144
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 358.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.43
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -30.05kcal/mol
Minimised FF energy -56.63kcal/mol

SASA & burial

✓ computed
SASA (unbound) 554.3Ų
Total solvent-accessible surface area of free ligand
BSA total 508.4Ų
Buried surface area upon binding
BSA apolar 352.9Ų
Hydrophobic contacts buried
BSA polar 155.5Ų
Polar contacts buried
Fraction buried 91.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1407.6Ų
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 810.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)