FAIRMol

KB_HAT_176

Pose ID 5518 Compound 593 Pose 100

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
T09
L. major DHFR-TS L. major
Ligand KB_HAT_176

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
35.8 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.17
Burial
90%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
4 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.400 kcal/mol/HA) ✓ Good fit quality (FQ -13.77) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Very high strain energy (35.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-44.800
kcal/mol
LE
-1.400
kcal/mol/HA
Fit Quality
-13.77
FQ (Leeson)
HAC
32
heavy atoms
MW
473
Da
LogP
3.29
cLogP
Strain ΔE
35.8 kcal/mol
SASA buried
90%
Lipo contact
81% BSA apolar/total
SASA unbound
724 Ų
Apolar buried
529 Ų

Interaction summary

HB 7 HY 24 PI 2 CLASH 5
Final rank2.590Score-44.800
Inter norm-0.793Intra norm-0.607
Top1000noExcludedno
Contacts19H-bonds7
Artifact reasongeometry warning; 8 clashes; 1 protein clash; 2 cofactor-context clashes; very favorable intra outlier; high strain Δ 35.8
Residues
NDP301 ALA32 ARG97 GLU43 ILE45 LEU94 LYS57 LYS95 MET53 PHE56 PHE91 PRO88 SER44 SER86 THR83 TYR162 VAL156 VAL31 VAL87

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap16Native recall0.76
Jaccard0.67RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.17

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
106 1.3407220211642157 -0.961998 -45.4744 2 19 0 0.00 0.00 - no Open
100 2.5897002349762537 -0.793386 -44.8002 7 19 16 0.76 0.17 - no Current
141 3.579369288789724 -0.845161 -50.681 5 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 -44.800kcal/mol
Ligand efficiency (LE) -1.4000kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -13.768
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 473.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.29
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 57.92kcal/mol
Minimised FF energy 22.17kcal/mol

SASA & burial

✓ computed
SASA (unbound) 724.2Ų
Total solvent-accessible surface area of free ligand
BSA total 652.2Ų
Buried surface area upon binding
BSA apolar 529.1Ų
Hydrophobic contacts buried
BSA polar 123.1Ų
Polar contacts buried
Fraction buried 90.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3363.9Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1645.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)