FAIRMol

Z49691086

Pose ID 494 Compound 138 Pose 494

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
T01
Human DHFR Human
Ligand Z49691086
PDB5SD8↗

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
26.7 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.20
Burial
86%
Hydrophobic fit
86%
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 (-0.585 kcal/mol/HA) ✓ Good fit quality (FQ -6.15) ✓ Good H-bonds (4 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ High strain energy (26.7 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (14)
Score
-23.992
kcal/mol
LE
-0.585
kcal/mol/HA
Fit Quality
-6.15
FQ (Leeson)
HAC
41
heavy atoms
MW
589
Da
LogP
5.84
cLogP
Strain ΔE
26.7 kcal/mol
SASA buried
86%
Lipo contact
86% BSA apolar/total
SASA unbound
867 Ų
Apolar buried
641 Ų

Interaction summary

HB 4 HY 24 PI 4 CLASH 3
Final rank1.178Score-23.992
Inter norm-0.635Intra norm0.050
Top1000noExcludedno
Contacts19H-bonds4
Artifact reasongeometry warning; 14 clashes; 2 protein contact clashes; 1 cofactor-context clash; moderate strain Δ 26.5
Residues
ALA10 ARG29 ASN65 GLU31 ILE61 ILE8 LEU23 LEU28 LEU68 NAP201 PHE32 PHE35 PRO27 PRO62 SER60 THR137 THR57 TYR34 VAL9

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

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 overlap15Native recall0.71
Jaccard0.60RMSD-
HB strict1Strict recall0.20
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
494 1.1779785607197466 -0.63534 -23.9924 4 19 15 0.71 0.20 - no Current
445 2.297742431915645 -0.478985 -17.4837 6 12 0 0.00 0.00 - no Open
487 2.791937129485576 -0.628302 -23.9607 1 22 18 0.86 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 -23.992kcal/mol
Ligand efficiency (LE) -0.5852kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.149
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 41HA

Physicochemical properties
Molecular weight 589.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.84
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 9.77kcal/mol
Minimised FF energy -16.90kcal/mol

SASA & burial

✓ computed
SASA (unbound) 867.2Ų
Total solvent-accessible surface area of free ligand
BSA total 747.6Ų
Buried surface area upon binding
BSA apolar 640.9Ų
Hydrophobic contacts buried
BSA polar 106.7Ų
Polar contacts buried
Fraction buried 86.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1808.3Ų
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 1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 620.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)