FAIRMol

MK216

Pose ID 1681 Compound 534 Pose 326

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 MK216

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 high Native mixed SASA done
Strain ΔE
15.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.40, Jaccard 0.32, H-bond role recall 0.00
Burial
90%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.867 kcal/mol/HA) ✓ Good fit quality (FQ -8.36) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Moderate strain (15.4 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (14)
Score
-25.997
kcal/mol
LE
-0.867
kcal/mol/HA
Fit Quality
-8.36
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
15.4 kcal/mol
SASA buried
90%
Lipo contact
81% BSA apolar/total
SASA unbound
694 Ų
Apolar buried
509 Ų

Interaction summary

HB 6 HY 24 PI 2 CLASH 2
Final rank1.523Score-25.997
Inter norm-0.968Intra norm0.102
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 14 clashes; 6 protein contact clashes
Residues
ARG48 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 PHE56 PHE91 PRO93 TRP47 VAL49

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 overlap8Native recall0.40
Jaccard0.32RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
263 1.0267699428225585 -1.16463 -31.7677 11 13 0 0.00 0.00 - no Open
248 1.0565759821753493 -1.05865 -27.2137 11 11 0 0.00 0.00 - no Open
275 1.158072578337196 -0.79049 -20.4723 4 16 0 0.00 0.00 - no Open
326 1.522628122716502 -0.968338 -25.9969 6 13 8 0.40 0.00 - no Current
244 1.708744967754064 -0.825708 -20.6159 5 19 1 0.05 0.00 - no Open
257 1.8345663825114074 -0.798505 -19.855 3 19 1 0.05 0.00 - no Open
309 1.905113599274035 -0.859805 -26.3343 3 12 0 0.00 0.00 - no Open
209 2.4824832058938013 -1.05337 -29.243 13 18 0 0.00 0.00 - no Open
204 2.663282674439042 -1.13906 -30.5138 11 18 0 0.00 0.00 - no Open
270 2.7066301048038337 -0.90359 -23.3047 8 16 0 0.00 0.00 - no Open
335 3.062936325722447 -0.858552 -27.4791 7 19 0 0.00 0.00 - no Open
224 3.0864929722424383 -0.941482 -26.4284 4 18 1 0.05 0.00 - no Open
308 3.1241016565923485 -1.04343 -27.852 6 10 6 0.30 0.00 - no Open
210 3.431812628247348 -1.01323 -26.2551 13 17 0 0.00 0.00 - no Open
200 4.283886601626247 -0.994469 -27.0487 13 17 0 0.00 0.00 - no Open
213 4.298392329825456 -0.999515 -28.3054 11 16 0 0.00 0.00 - no Open
307 4.451695165235262 -0.776336 -19.1475 5 13 0 0.00 0.00 - no Open
249 5.404412263953654 -0.824137 -19.6852 7 12 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 -25.997kcal/mol
Ligand efficiency (LE) -0.8666kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.359
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.80
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 52.04kcal/mol
Minimised FF energy 36.68kcal/mol

SASA & burial

✓ computed
SASA (unbound) 693.7Ų
Total solvent-accessible surface area of free ligand
BSA total 626.8Ų
Buried surface area upon binding
BSA apolar 508.9Ų
Hydrophobic contacts buried
BSA polar 117.8Ų
Polar contacts buried
Fraction buried 90.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1589.8Ų
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 804.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)